Vesicle-associated proteins

ABSTRACT

Various embodiments of the invention provide human vesicle-associated proteins (VAP) and polynucleotides which identify and encode VAP. Embodiments of the invention also provide expression vectors, host cells, antibodies, agonists, and antagonists. Other embodiments provide methods for diagnosing, treating, or preventing disorders associated with aberrant expression of VAP.

TECHNICAL FIELD

[0001] The invention relates to novel nucleic acids, vesicle-associatedproteins encoded by these nucleic acids, and to the use of these nucleicacids and proteins in the diagnosis, treatment, and prevention ofvesicle trafficking disorders, autoimmune/inflammatory disorders, andcancer. The invention also relates to the assessment of the effects ofexogenous compounds on the expression of nucleic acids andvesicle-associated proteins.

BACKGROUND OF THE INVENTION

[0002] Eukaryotic cells are bound by a lipid bilayer membrane andsubdivided into functionally distinct, membrane-bound compartments. Themembranes maintain the essential differences between the cytosol, theextracellular environment, and the lumenal space of each intracellularorganelle. As lipid membranes are highly impermeable to most polarmolecules, transport of essential nutrients, metabolic waste products,cell signaling molecules, macromolecules, and proteins across lipidmembranes and between organelles must be mediated by a variety oftransport-associated molecules.

[0003] Integral membrane proteins, secreted proteins, and proteinsdestined for the lumen of organelles are synthesized within theendoplasmic reticulum (ER), delivered to the Golgi complex forpost-translational processing and sorting, and then transported tospecific intracellular and extracellular destinations. Material isinternalized from the extracellular environment by endocytosis, aprocess essential for transmission of neuronal, metabolic, andproliferative signals; uptake of many essential nutrients; and defenseagainst invading organisms. This intracellular and extracellularmovement of protein molecules is termed vesicle trafficking. Traffickingis accomplished by the packaging of protein molecules into specializedvesicles which bud from the donor organelle membrane and fuse to thetarget membrane (Rothman, J. E and F. T. Wieland (1996) Science272:227-234).

[0004] The transport of proteins across the ER membrane involves aprocess that is simnilar in bacteria, yeast, and mammals (Gorlich, D. etal. (1992) Cell 71:489-503). In mammalian systems, transport isinitiated by the action of a cytoplasmic signal recognition particle(SRP) which recognizes a signal sequence on a growing, nascentpolypeptide and binds the polypeptide and its ribosome complex to the ERmembrane through an SRP receptor located on the ER membrane. The signalpeptide is cleaved and the ribosome complex, together with the attachedpolypeptide, becomes membrane bound. The polypeptide is subsequentlytranslocated across the ER membrane and into a vesicle (Blobel, G. andB. Dobberstein (1975) J. Cell Biol. 67:852-862).

[0005] Proteins implicated in the translocation of polypeptides acrossthe ER membrane in yeast include SEC61p, SEC62p, and SEC63p. Mutationsin the genes encoding these proteins lead to defects in thetranslocation process. SEC61 may be of particular importance sincecertain mutations in the gene for this protein inhibit the translocationof many proteins (Gorlich et al., supra).

[0006] Marrmalian homologs of yeast SEC61 (mSEC61) have been identifiedin dog and rat (Gorlich et al., supra). Mammalian SEC61 is alsostructurally similar to SECYp, the bacterial cytoplasmic membranetranslocation protein. mSEC61 is found in tight association withmembrane-bound ribosomes. This association is induced bymembrane-targeting of nascent polypeptide chains and is weakened bydissociation of the ribosomes into their constituent subunits. mSEC61 ispostulated to be a component of a putative protein-conducting channel,located in the ER membrane, to which nascent polypeptides aretransferred following the completion of translation by ribosomes(Gorlich et al., supra).

[0007] Several steps in the transit of material along the secretory andendocytic pathways require the formation of transport vesicles.Specifically, vesicles form at the transitional endoplasmic reticulum(tER), the rim of Golgi cisternae, the face of the Trans-Golgi Network(TGN), the plasma membrane (PM), and tubular extensions of theendosomes. Vesicle formation occurs when a region of membrane buds offfrom the donor organelle. The membrane-bound vesicle contains proteinsto be transported and is surrounded by a proteinaceous coat, thecomponents of which are recruited from the cytosol. Vesicle formationbegins with the budding of a vesicle out of a donor organelle. Theinitial budding and coating processes are controlled by a cytosolicras-like GTP-binding protein, ADP-ribosylating factor (Arf), and adapterproteins (APs). Different isoforms of both Arf and AP are involved atdifferent sites of budding. For example, Arfs 1, 3, and 5 are requiredfor Golgi budding, Arf4 for endosomal budding, and Arf6 for plasmamembrane budding. Two different classes of coat protein have also beenidentified. Clathrin coats form on vesicles derived from the TGN and PM,whereas coatomer (COP) coats form on vesicles derived from the ER andGolgi (Mellman, I. (1996) Annu. Rev. Cell Dev. Biol. 12:575625).

[0008] In clathrin-based vesicle formation, APs bring vesicle cargo andcoat proteins together at the surface of the budding membrane. APs areheterotetrameric complexes composed of two large chains (α, γ, δ, or ε,and β), a medium chain (μ), and a small chain (σ). Clathrin binds to APsvia the carboxy-terminal appendage domain of the β-adaptin subunit (LeBourgne, R. and B. Hoflack (1998) Curr. Opin. Cell. Biol. 10:499-503).AP-1 functions in protein sorting from the TGN and endosomes tocompartments of the endosomal/lysosomal system. AP-2 functions inclathrin-mediated endocytosis at the plasma membrane, while AP-3 isassociated with endosomes and/or the TGN and recruits integral membraneproteins for transport to lysosomes and lysosome-related organelles. Therecently isolated AP-4 complex localizes to the TGN or a neighboringcompartment and may play a role in sorting events thought to take placein post-Golgi compartments (Dell'Angelica, E. C. et al. (1999) J. Biol.Chem. 274:7278-7285). Cytosolic GTP-bound Arf is also incorporated intothe vesicle as it forms. Another GTP-binding protein, dynamin, forms aring complex around the neck of the forming vesicle and provides themechanochemical force required to release the vesicle from the donormembrane. The coated vesicle complex is then transported through thecytosol. During the transport process, Arf-bound GTP is hydrolyzed toGDP and the coat dissociates from the transport vesicle (West, M. A. etal. (1997) J. Cell Biol. 138:1239-1254).

[0009] Coatomer (COP) coats form on vesicles derived from the ER andGolgi. COP coats can further be distinguished as COPI, involved inretrograde traffic through the Golgi to the ER, and COPII, involved inanterograde traffic from the ER to the Golgi. The COP coat consists oftwo major components, a GTP-binding protein (Arf or Sar) and coatprotomer (coatomer). Coatomer is an equimolar complex of seven proteins,termed alpha-, beta-, beta′-, gamma-, delta-, epsilon- and zeta-COP. Thecoatomer complex binds to dilysine motifs contained on the cytoplasmictails of integral membrane proteins. These include thedilysine-containing retrieval motif of membrane proteins of the ER anddibasic/diphenylamine motifs of members of the p24 family. The p24family of type I membrane proteins represent the major membrane proteinsof COPI vesicles (Harter, C. and F. T. Wieland (1998) Proc. Natl. Acad.Sci. USA 95:11649-11654).

[0010] Vesicles can undergo homotypic or heterotypic fusion. Moleculesrequired for appropriate targeting and fusion of vesicles includeproteins in the vesicle membrane, the target membrane, and proteinsrecruited from the cytosol. During budding of the vesicle from the donorcompartment, an integral membrane protein, VAMP (vesicle-associatedmembrane protein) is incorporated into the vesicle. Soon after thevesicle uncoats, a cytosolic prenylated GTP-binding protein, Rab, isinserted into the vesicle membrane. In the vesicle membrane, GTP-boundRab interacts with VAMP.

[0011] The amino acid sequences of Rab proteins reveal conservedGTP-binding domains characteristic of Ras superfamnily members. Rabproteins also have a highly variable amino terminus containingmembrane-specific signal information and a prenylated carboxy terminuswhich determines the target membrane to which the Rab proteins anchor.More than 30 Rab proteins have been identified in a variety of species,and each has a characteristic intracellular location and distincttransport function. In particular, Rab1 and Rab2 are important inER-to-Golgi transport; Rab3 transports secretory vesicles to theextracellular membrane; Rab5 is localized to endosomes and regulates thefusion of early endosomes into late endosomes; Rab6 is specific to theGolgi apparatus and regulates intra-Golgi transport events; Rab7 andRab9 stimulate the fusion of late endosomes and Golgi vesicles withlysosomes, respectively; and Rab10 mediates vesicle fusion from themedial Golgi to the trans Golgi. Mutant forms of Rab proteins are ableto block protein transport along a given pathway or alter the sizes ofentire organelles. Therefore, Rabs play key regulatory roles in membranetrafficking (Schimmoller, I. S. and S. R. Pfeffer (1998) J. Biol. Chem.243:22161-22164).

[0012] The function of Rab proteins in vesicular transport requires thecooperation of many other proteins. Specifically, the membrane-targetingprocess is assisted by a series of escort proteins (Khosravi-Par, R. etal. (1991) Proc. Natl. Acad. Sci. USA 88:6264-6268). In the medialGolgi, it has been shown that GTP-bound Rab proteins initiate thebinding of VAMP-like proteins of the transport vesicle to syntaxin-likeproteins on the acceptor membrane, which subsequently triggers a cascadeof protein-binding and membrane-fusion events. After transport,GTPase-activating proteins (GAPs) in the target membrane are responsiblefor converting the GTP-bound Rab proteins to their GDP-bound state. Andfinally a cytosolic protein, guanine-nucleotide dissociation inhibitor(GDI), removes GDP-bound Rab from the vesicle membrane.

[0013] Docking of the transport vesicle with the target membraneinvolves the formation of a complex between the vesicle SNAP receptor(v-SNARE), target membrane (t-) SNAREs, and certain other membrane andcytosolic proteins. Many of these other proteins have been identifiedalthough their exact functions in the docking complex remain uncertain(Tellam, J. T. et al. (1995) J. Biol. Chem. 270:5857-5863; Hata, Y. andT. C. Sudhof (1995) J. Biol. Chem. 270:13022-13028). N-ethylmaleimidesensitive factor (NSF) and soluble NSF-attachment protein (α-SNAP andβ-SNAP) are two such proteins that are conserved from yeast to man andfunction in most intracellular membrane fusion reactions. Many of thesemembrane and cytosolic proteins contain an AAA protein family signaturedomain. The AAA protein family signature consists of a large family ofATPases whose key feature is that they share a conserved region ofapproximately 200 amino acids that contains an ATP-binding site. Thisfamily is called AAA, for ‘A’ TPases ‘A’ ssociated with diverse cellular‘A’ ctivities. The proteins that belong to this family either containone or two AAA domains. Mammalian NSF contains two AAA domains, involvedin intracellular transport between the endoplasmic reticulum and Golgi,as well as between different Golgi cisternae. Secl represents a familyof yeast proteins that function at many different stages in thesecretory pathway including membrane fusion. Recently, mammalianhomologs of Sec I, called Munc-18 proteins, have been identified(Katagiri, H. et al. (1995) J. Biol. Chem. 270:49634966; Hata andSudhof, supra). Sec22p is a yeast v-SNARE required for transport betweenthe ER and the Golgi apparatus. Marnmalian sec22 homologs have beenidentified in humans, rats, mice, and hamsters (Tang, B. L. et al.(1998) Biochem. Biophys. Res. Commun. 243:885-91; and referenceswithin).

[0014] The SNARE complex involves three SNARE molecules, one in thevesicular membrane and two in the target membrane. Together they form arod-shaped complex of four α-helical coiled-coils. The membraneanchoring domains of all three SNAREs project from one end of the rod.This complex is similar to the rod-like structures formed by fusionproteins characteristic of the enveloped viruses, such as myxovirus,influenza, filovirus (Ebola), and the HW and SIV retroviruses (Skehel,J. J. and D. C. Wiley (1998) Cell 95:871-874). It has been proposed thatthe SNARE complex is sufficient for membrane fusion, suggesting that theproteins which associate with the complex provide regulation over thefusion event (Weber, T. et al. (1998) Cell 92:759-772). For example, inneurons, which exhibit regulated exocytosis, docked vesicles do not fusewith the presynaptic membrane until depolarization, which leads to aninflux of calcium (Bennett, M. K. and R. H. Scheller (1994) Annu. Rev.Biochem. 63:63-100). Synaptotagmin, an integral membrane protein in thesynaptic vesicle, associates with the t-SNARE syntaxin in the dockingcomplex. Synaptotagmin binds calcium in a complex with negativelycharged phospholipids, which allows the cytosolic SNAP protein todisplace synaptotagmin from syntaxin and fusion to occur. Thus,synaptotagmin is a negative regulator of fusion in the neuron(Littleton, J. T. et al. (1993) Cell 74:1125-1134). The most abundantmembrane protein of synaptic vesicles appears to be the glycoproteinsynaptophysin, a 38 kDa protein with four transmembrane domains.Although the function of synaptophysin is not known, its calcium-bindingability, tyrosine phosphorylation, and widespread distribution in neuraltissues suggest a potential role in neurosecretion (Bennett andScheller, supra). The synaptojanin family of proteins have beenimplicated in synaptic vesicle recycling and actin function.Synaptojanins are phosphoinositide phosphatases predominantly expressedin the nervous system. One form of synaptojanin, synaptojanin 2A, istargeted to mitochondria by the interaction with the PDZ-domain of amitochondrial outer membrane protein (Nemoto, Y. and P. De Camilli(1999) EMBO J. 18:2991-3006).

[0015] The transport of proteins into and out of vesicles relies oninteractions between cell membranes and a supporting membranecytoskeleton consisting of spectrin and other proteins. A large familyof related proteins called ankyrins participate in the transport processby binding to the membrane skeleton protein spectrin and to a protein inthe cell membrane called band 3, a component of an anion channel in thecell membrane. Ankyrins therefore function as a critical link betweenthe cytoskeleton and the cell membrane.

[0016] Originally found in association with erythroid cells, ankyrinsare also found in other tissues as well (Birkenmeier, C. S. et al.(1993) J. Biol. Chem. 268:9533-9540). Ankyrins are large proteins (1800amino acids) containing an N-terminal, 89 kDa domain that binds the cellmembrane proteins band 3 and tubulin, a central 62 kDa domain that bindsthe cytoskeletal proteins spectrin and vimentin, and a C-terminal, 55kDa regulatory domain that functions as a modifier of the bindingactivities of the other two domains. Individual genes for ankyrin areable to produce multiple ankyrin isoforms by various insertions anddeletions. These isoforms are of nearly identical size but may havedifferent functions. In addition, smaller transcripts are produced whichare missing large regions of the coding sequences from the N-terminal(band 3 binding), and central (spectrin binding) domains. The existenceof such a large family of ankyrin proteins and the observation that morethan one type of ankyrin may be expressed in the same cell type suggeststhat ankyrins may have more specialized functions than simply bindingthe membrane skeleton to the plasma membrane (Birkenmeier et al.,supra).

[0017] In humans, two isoforms of ankyrin are expressed, alternatively,in developing erythroids and mature erythroids, respectively (Lambert,S. et. al. (1990) Proc. Natl. Acad. Sci. USA 87:1730-1734). A deficiencyin erythroid spectrin and ankyrin has been associated with the hemolyticanemia, hereditary spherocytosis (Coetzer, T. L. et al. (1988) New Engl.J. Med. 318:230-234).

[0018] Correct trafficking of proteins is of particular importance forthe proper function of epithelial cells, which are polarized intodistinct apical and basolateral domains containing different cellmembrane components such as lipids and membrane-associated proteins.Certain proteins are flexible and may be sorted to the basolateral orapical side depending upon cell type or growth conditions. For example,the kidney anion exchanger (kAE1) can be retargeted from the apical tothe basolateral domain if cells are plated at higher density. Theprotein kanadaptin was isolated as a protein which binds to thecytoplasmic domain of kAE1. It also colocalizes with kAE1 in vesicles,but not in the membrane, suggesting that kanadaptin's function is toguide kAE1-containing vesicles to the basolateral target membrane (Chen,J. et al. (1998) J. Biol. Chem. 273:1038-1043).

[0019] Vesicle trafficking is crucial in the process ofneurotransmission. Synaptic vesicles carry neurotransmitter moleculesfrom the cytoplasm of a neuron to the synapse. Rab3s are a family ofGTP-binding proteins located on synaptic vesicles. The RIM family ofproteins are thought to be effectors for Rab3s (Wang, Y. et al. (2000)J. Biol. Chem. 275:20033-20044). Rabphilin-3 is a synaptic vesicleprotein. Granuphilins are proteins with homology to rabphilins, and mayhave a unique role in exocytosis (Wang, J. et al. (1999) J. Biol. Chem.274:28542-28548).

[0020] As studied in nematodes, vesicle-associated proteins are alsoinvolved in sperm motility. Major sperm protein (MSP) contributes tosperm pseudopodial movement by forming a cytosolic filament network thattranslocates vesicles to the plasma membrane (Italiano, J. E. et al.(1996) Cell 84:105-114; Roberts, T. M. et al. (1998) J. Cell Biol.140:367-75).

[0021] The etiology of numerous human diseases and disorders can beattributed to defects in the trafficking of proteins to organelles orthe cell surface. Defects in the trafficking of membrane-bound receptorsand ion channels are associated with cystic fibrosis (cystic fibrosistransmembrane conductance regulator; CFTR), glucose-galactosemalabsorption syndrome (Na⁺/glucose cotransporter), hypercholesterolemia(low-density lipoprotein (LDL) receptor), and forms of diabetes mellitus(insulin receptor). Abnormal hormonal secretion is linked to disordersincluding diabetes insipidus (vasopressin), hyper- and hypoglycemia(insulin, glucagon), Grave's disease and goiter (thyroid hormone), andCushing's and Addison's diseases (adrenocorticotropic hormone; ACT1H).

[0022] Cancer cells secrete excessive amounts of hormones or otherbiologically active peptides. Disorders related to excessive secretionof biologically active peptides by tumor cells include: fastinghypoglycemia due to increased insulin secretion from insulinoma-isletcell tumors; hypertension due to increased epinephrine andnorepinephrine secreted from pheochromocytomas of the adrenal medullaand sympathetic paraganglia; and carcinoid syndrome, which includesabdominal cramps, diarrhea, and valvular heart disease, caused byexcessive amounts of vasoactive substances (serotonin, bradykinin,histamine, prostaglandins, and polypeptide hormones) secreted fromintestinal tumors. Ectopic synthesis and secretion of biologicallyactive peptides (peptides not expected from a tumor) includes ACTH andvasopressin in lung and pancreatic cancers; parathyroid hormone in lungand bladder cancers; calcitonin in lung and breast cancers; andthyroid-stimulating hormone in medullary thyroid carcinoma.

[0023] Various human pathogens alter host cell protein traffickingpathways to their own advantage. For example, the HIV protein Nefdownregulates cell-surface expression of CD4 molecules by acceleratingtheir endocytosis through clathrin coated pits. This function of Nef isimportant for the spread of HIV from the infected cell (Harris, M.(1999) Curr. Biol. 9:R449-R461). A recently identified human protein,Nef-associated factor 1 (Naf1), a protein with four extended coiled-coildomains, has been found to associate with Nef. Overexpression of Naf1increased cell surface expression of CD4, an effect which could besuppressed by Nef (Fukushi, M. et al. (1999) FEBS Lett. 442:83-88).

[0024] Expression Profiling

[0025] Microarrays are analytical tools used in bioanalysis. Amicroarray has a plurality of molecules spatially distributed over, andstably associated with, the surface of a solid support. Microarrays ofpolypeptides, polynucleotides, and/or antibodies have been developed andfind use in a variety of applications, such as gene sequencing,monitoring gene expression, gene mapping, bacterial identification, drugdiscovery, and combinatorial chemistry.

[0026] One area in particular in which microarrays find use is in geneexpression analysis. Array technology can provide a simple way toexplore the expression of a single polymorphic gene or the expressionprofile of a large number of related or unrelated genes. When theexpression of a single gene is examined, arrays are employed to detectthe expression of a specific gene or its variants. When an expressionprofile is examined, arrays provide a platform for identifying genesthat are tissue specific, are affected by a substance being tested in atoxicology assay, are part of a signaling cascade, carry outhousekeeping functions, or are specifically related to a particulargenetic predisposition, condition, disease, or disorder.

[0027] Genes Expressed in Breast Cancer

[0028] The potential application of gene expression profiling isrelevant to improving diagnosis, prognosis, and treatment of disease.For example, both the levels and sequences expressed in tissues fromsubjects with breast cancer may be compared with the levels andsequences expressed in normal tissue.

[0029] There are more than 180,000 new cases of breast cancer diagnosedeach year, and the mortality rate for breast cancer approaches 10% ofall deaths in females between the ages of 45-54 (Gish, K. (1999) AWISMagazine 28:7-10). However the survival rate based on early diagnosis oflocalized breast cancer is extremely high (97%), compared with theadvanced stage of the disease in which the tumor has spread beyond thebreast (22%). Current procedures for clinical breast examination arelacking in sensitivity and specificity, and efforts are underway todevelop comprehensive gene expression profiles for breast cancer thatmay be used in conjunction with conventional screening methods toimprove diagnosis and prognosis of this disease (Perou, C. M. et al.(2000) Nature 406:747-752).

[0030] Breast cancer is a genetic disease commonly caused by mutationsin cellular disease. Mutations in two genes, BRCA1 and BRCA2, are knownto greatly predispose a woman to breast cancer and may be passed on fromparents to children (Gish, supra). However, this type of hereditarybreast cancer accounts for only about 5% to 9% of breast cancers, whilethe vast majority of breast cancer is due to noninherited mutations thatoccur in breast epithelial cells.

[0031] A good deal is already known about the expression of specificgenes associated with breast cancer. For example, the relationshipbetween expression of epidermal growth factor (EGF) and its receptor,EGFR, to human mammary carcinoma has been particularly well studied.(See Khazaie et al., supra, and references cited therein for a review ofthis area.) Overexpression of EGFR, particularly coupled withdown-regulation of the estrogen receptor, is a marker of poor prognosisin breast cancer patients. In addition, EGFR expression in breast tumormetastases is frequently elevated relative to the primary tumor,suggesting that EGFR is involved in tumor progression and metastasis.This is supported by accumulating evidence that EGF has effects on cellfunctions related to metastatic potential, such as cell motility,chemotaxis, secretion and differentiation. Changes in expression ofother members of the erbB receptor family, of which EGFR is one, havealso been implicated in breast cancer. The abundance of erbB receptors,such as BER-2/neu, BER-3, and HER-4, and their ligands in breast cancerpoints to their functional importance in the pathogenesis of thedisease, and may therefore provide targets for therapy of the disease(Bacus, S. S. et al. (1994) Am. J. Clin. Pathol. 102:S13-S24). Otherknown markers of breast cancer include a human secreted frizzled proteinmRNA that is downregulated in breast tumors; the matrix Gla proteinwhich is overexpressed is human breast carcinoma cells; Drgl or RTP, agene whose expression is diminished in colon, breast, and prostatetumors; maspin, a tumor suppressor gene downregulated in invasive breastcarcinomas; and CaN19, a member of the S100 protein family, all of whichare down regulated in mammary carcinoma cells relative to normal mammaryepithelial cells (Zhou, Z. et al. (1998) Int. J. Cancer 78:95-99; Chen,L. et al. (1990) Oncogene 5:1391-1395; Uhix, W. et al (1999) FBBS Lett.455:23-26; Sager, R. et al. (1996) CuiT. Top. Microbiol. Immunol.213:51-64; and Lee, S. W. et al. (1992) Proc. Natl. Acad. Sci. USA89:2504-2508).

[0032] Cell lines derived from human mammary epithelial cells at variousstages of breast cancer provide a useful model to study the process ofmalignant transformation and tumor progression as it has been shown thatthese cell lines retain many of the properties of their parental tumorsfor lengthy culture periods (Wistuba, I. I. et al. (1998) Clin. CancerRes. 4:2931-2938). Such a model is particularly useful for comparingphenotypic and molecular characteristics of human mammary epithelialcells at various stages of malignant transformation.

[0033] Genes Expressed in Prostate Cancer

[0034] The potential application of gene expression profiling is alsorelevant to improving diagnosis, prognosis, and treatment of disease.For example, both the levels and sequences expressed in tissues fromsubjects with prostate cancer may be compared with the levels andsequences expressed in normal tissue.

[0035] Prostate cancer is a common malignancy in men over the age of 50,and the incidence increases with age. In the US, there are approximately132,000 newly diagnosed cases of prostate cancer and more than 33,000deaths from the disorder each year.

[0036] Once cancer cells arise in the prostate, they are stimulated bytestosterone to a more rapid growth. Thus, removal of the testes canindirectly reduce both rapid growth and metastasis of the cancer. Over95 percent of prostatic cancers are adenocarcinomas which originate inthe prostatic acini. The remaining 5 percent are divided betweensquamous cell and transitional cell carcinomas, both of which arise inthe prostatic ducts or other parts of the prostate gland.

[0037] As with most cancers, prostate cancer develops through amultistage progression ultimately resulting in an aggressive, metastaticphenotype. The initial step in tumor progression involves thehyperproliferation of normal luminal and/or basal epithelial cells thatbecome hyperplastic and evolve into early-stage tumors. The early-stagetumors are localized in the prostate but eventually may metastasize,particularly to the bone, brain or lung. About 80% of these tumorsremain responsive to androgen treatment, an important hormonecontrolling the growth of prostate epithelial cells. However, in itsmost advanced state, cancer growth becomes androgen-independent andthere is currently no known treatment for this condition.

[0038] A primary diagnostic marker for prostate cancer is prostatespecific antigen (PSA). PSA is a tissue-specific serine protease almostexclusively produced by prostatic epithelial cells. The quantity of PSAcorrelates with the number and volume of the prostatic epithelial cells,and consequently, the levels of PSA are an excellent indicator ofabnormal prostate growth. Men with prostate cancer exhibit an earlylinear increase in PSA levels followed by an exponential increase priorto diagnosis. However, since PSA levels are also influenced by factorssuch as inflammation, androgen and other growth factors, some scientistsmaintain that changes in PSA levels are not useful in detectingindividual cases of prostate cancer.

[0039] Current areas of cancer research provide additional prospects formarkers as well as potential therapeutic targets for prostate cancer.Several growth factors have been shown to play a critical role in tumordevelopment, growth, and progression. The growth factors EpidermalGrowth Factor (EGF), Fibroblast Growth Factor (FGF), and Tumor GrowthFactor alpha (TGFα) are important in the growth of normal as well ashyperproliferative prostate epithelial cells, particularly at earlystages of tumor development and progression, and affect signalingpathways in these cells in various ways (Lin, J. et al. (1999) CancerRes. 59:2891-2897; Putz, T. et al. (1999) Cancer Res. 59:227-233). TheTGF-0 family of growth factors are generally expressed at increasedlevels in human cancers and the high expression levels in many casescorrelates with advanced stages of malignancy and poor survival (Gold,L. I. (1999) Crit. Rev. Oncog. 10:303-360). Finally, there are humancell lines representing both the androgen-dependent stage of prostatecancer (LNCap) as well as the androgen-independent, hormone refractorystage of the disease (PC3 and DU145) that have proved useful in studyinggene expression patterns associated with the progression of prostatecancer, and the effects of cell treatments on these expressed genes(Chung, T. D. (1999) Prostate 15:199-207).

[0040] Genes Expressed in Adipocyte Differentiation

[0041] The potential application of gene expression profiling isrelevant to improving diagnosis, prognosis, and treatment of disease.For example, both the levels and sequences expressed in tissues fromsubjects with obesity or type II diabetes may be compared with thelevels and sequences expressed in normal tissue.

[0042] The primary function of adipose tissue is the ability to storeand release fat during periods of feeding and fasting. White adiposetissue is the major energy reserve in periods of fasting, and itsreserve is mobilized during energy deprivation. Adipose tissue is one ofthe primary target tissues for insulin, and adipogenesis and insulinresistance are linked in type II diabetes, non-insulin dependentdiabetes mellitus (NIDDM). Cytologically the conversion of apreadipocytes into mature adipocytes is characterized by deposition offat droplets around the nuclei. The conversion process in vivo can beinduced by thiazolidinediones (TZDs) and other PPARγ agonists (Adams, M.et al. (1997) J. Clin. Invest. 100:3149-3153) which also lead toincreased sensitivity to insulin and reduced plasma glucose and bloodpressure.

[0043] Thiazolidinediones (TZDs) act as agonists for theperoxisome-proliferator-activated receptor gamma (PPARγ), a member ofthe nuclear hormone receptor superfamily. TZDs reduce hyperglycemia,hyperinsulinemia, and hypertension, in part by promoting glucosemetabolism and inhibiting gluconeogenesis. Roles for PPARγ and itsagonists have been demonstrated in a wide range of pathologicalconditions including diabetes, obesity, hypertension, atherosclerosis,polycystic ovarian syndrome, and cancers such as breast, prostate,liposarcoma, and colon cancer.

[0044] The mechanism by which TZDs and other PPARγ agonists enhanceinsulin sensitivity is not fully understood, but may involve the abilityof PPARγ to promote adipogenesis. When ectopically expressed in culturedpreadipocytes, PPARγ is a potent inducer of adipocyte differentiation.TZDs, in combination with insulin and other factors, can also enhancedifferentiation of human preadipocytes in culture (Adams, et al.,supra). The relative potency of different TZDs in promoting adipogenesisin vitro is proportional to both their insulin sensitizing effects invivo, and their ability to bind and activate PPARγ in vitro.Interestingly, adipocytes derived from omental adipose depots arerefractory to the effects of TZDs. It has therefore been suggested thatthe insulin sensitizing effects of TZDs may result from their ability topromote adipogenesis in subcutaneous adipose depots (Adams et al.,supra). Further, dominant negative mutations in the PPARγ gene have beenidentified in two non-obese subjects with severe insulin resistance,hypertension, and overt non-insulin dependent diabetes mellitus (NEDDM)(Barroso, I. et al. (1998) Nature 402:880-883).

[0045] NIDDM is the most common form of diabetes mellitus, a chronicmetabolic disease that affects 143 million people worldwide. NHDDM ischaracterized by abnormal glucose and lipid metabolism that result froma combination of peripheral insulin resistance and defective insulinsecretion. NIDDM has a complex, progressive etiology and a high degreeof heritability. Numerous complications of diabetes including heartdisease, stroke, renal failure, retinopathy, and peripheral neuropathycontribute to the high rate of morbidity and mortality.

[0046] At the molecular level, PPARγ functions as a ligand activatedtranscription factor. In the presence of ligand, PPARγ forms aheterodimer with the retinoid X receptor (RXR) which then activatestranscription of target genes containing one or more copies of a PPARγresponse element (PPRE). Many genes important in lipid storage andmetabolism contain PPREs and have been identified as PPARγ targets,including PEPCK, aP2, LPL, ACS, and FAT-P (Auwerx, J. (1999)Diabetologia 42:1033-1049). Multiple ligands for PPARγ have beenidentified. These include a variety of fatty acid metabolites; syntheticdrugs belonging to the TZD class, such as Pioglitazone and Rosiglitazone(BRL49653); and certain non-glitazone tyrosine analogs such as G1262570and GW1929. The prostaglandin derivative 15-dPGJ2 is a potent endogenousligand for PPARγ.

[0047] Expression of PPARγ is very high in adipose but barely detectablein skeletal muscle, the primary site for insulin stimulated glucosedisposal in the body. PPARγ is also moderately expressed in largeintestine, kidney, liver, vascular smooth muscle, hematopoietic cells,and macrophages. The high expression of PPARγ in adipose suggests thatthe insulin sensitizing effects of TZDs may result from alterations inthe expression of one or more PPARγ regulated genes in adipose tissue.

[0048] Identification of PPARγ target genes will contribute to betterdrug design and the development of novel therapeutic strategies fordiabetes, obesity, and other conditions.

[0049] Systematic attempts to identify PPARγ target genes have been madein several rodent models of obesity and diabetes (Suzuki, A. et al.(2000) Jpn. J. Pharmacol. 84:113-123; Way, J. M. et al. (2001)Endocrinology 142:1269-1277). However, a serious drawback of the rodentgene expression studies is that significant differences exist betweenhuman and rodent models of adipogenesis, diabetes, and obesity (Taylor,S. I. (1999) Cell 97:9-12; Gregoire, F. M. et al. (1998) Physiol.Reviews 78:783-809). Therefore, an unbiased approach to identifying TZDregulated genes in primary cultures of human tissues is necessary tofully elucidate the molecular basis for diseases associated with PPARγactivity.

[0050] The majority of research in adipocyte biology to date has beendone using transformed mouse preadipocyte cell lines. The culturecondition, which stimulates mouse preadipocyte differentiation isdifferent from that for inducing human primary preadipocytedifferentiation. In addition, primary cells are diploid and maytherefore reflect the in vivo context better than aneuploid cell lines.Understanding the gene expression profile during adipogenesis in humanwill lead to understanding the fundamental mechanism of adiposityregulation. Furthermore, through comparing the gene expression profilesof adipogenesis between donor with normal weight and donor with obesity,identification of crucial genes, potential drug targets for obesity andtype H diabetes, will be possible.

[0051] There is a need in the art for new compositions, includingnucleic acids and proteins, for the diagnosis, prevention, and treatmentof vesicle trafficking disorders, autoimmune/inflammatory disorders, andcancer.

SUMMARY OF THE INVENTION

[0052] Various embodiments of the invention provide purifiedpolypeptides, vesicle-associated proteins, referred to collectively as‘VAP’ and individually as ‘VAP-1,’ ‘VAP-2,’ ‘VAP-3,’ ‘VAP-4,’ ‘VAP-5,’‘VAP-6,’ ‘VAP-7,’ ‘VAP-8,’ ‘VAP-9,’ ‘VAP-10,’ ‘VAP-11,’ ‘VAP-12,’‘VAP-13,’ ‘VAP-14,’ ‘VAP-15,’ ‘VAP-16,’ ‘VAP-17,’ ‘VAP-18,’ ‘VAP-19,’and ‘VAP-20’ and methods for using these proteins and their encodingpolynucleotides for the detection, diagnosis, and treatment of diseasesand medical conditions. Embodiments also provide methods for utilizingthe purified vesicle-associated proteins and/or their encodingpolynucleotides for facilitating the drug discovery process, includingdetermination of efficacy, dosage, toxicity, and pharmacology. Relatedembodiments provide methods for utilizing the purifiedvesicle-associated proteins and/or their encoding polynucleotides forinvestigating the pathogenesis of diseases and medical conditions.

[0053] An embodiment provides an isolated polypeptide selected from thegroup consisting of a) a polypeptide comprising an amino acid sequenceselected from the group consisting of SEQ ID NO:1-20, b) a polypeptidecomprising a naturally occurring amino acid sequence at least 90%identical or at least about 90% identical to an amino acid sequenceselected from the group consisting of SEQ ID NO: 1-20, c) a biologicallyactive fragment of a polypeptide having an amino acid sequence selectedfrom the group consisting of SEQ ID NO:1-20, and d) an immunogenicfragment of a polypeptide having an amino acid sequence selected fromthe group consisting of SEQ ID NO:1-20. Another embodiment provides anisolated polypeptide comprising an amino acid sequence of SEQ IDNO:1-20.

[0054] Still another embodiment provides an isolated polynucleotideencoding a polypeptide selected from the group consisting of a) apolypeptide comprising an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20, b) a polypeptide comprising a naturallyoccurring amino acid sequence at least 90% identical or at least about90% identical to an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20, c) a biologically active fragment of apolypeptide having an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20, and d) an immunogenic fragment of apolypeptide having an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20. In another embodiment, the polynucleotideencodes a polypeptide selected from the group consisting of SEQ IDNO:1-20. In an alternative embodiment, the polynucleotide is selectedfrom the group consisting of SEQ ID NO:21-40.

[0055] Still another embodiment provides a recombinant polynucleotidecomprising a promoter sequence operably linked to a polynucleotideencoding a polypeptide selected from the group consisting of a) apolypeptide comprising an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20, b) a polypeptide comprising a naturallyoccurring amino acid sequence at least 90% identical or at least about90% identical to an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20, c) a biologically active fragment of apolypeptide having an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20, and d) an immunogenic fragment of apolypeptide having an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20. Another embodiment provides a celltransformed with the recombinant polynucleotide. Yet another embodimentprovides a transgenic organism comprising the recombinantpolynucleotide.

[0056] Another embodiment provides a method for producing a polypeptideselected from the group consisting of a) a polypeptide comprising anamino acid sequence selected from the group consisting of SEQ IDNO:1-20, b) a polypeptide comprising a naturally occurring amino acidsequence at least 90% identical or at least about 90% identical to anamino acid sequence selected from the group consisting of SEQ IDNO:1-20, c) a biologically active fragment of a polypeptide having anamino acid sequence selected from the group consisting of SEQ IDNO:1-20, and d) an immunogenic fragment of a polypeptide having an aminoacid sequence selected from the group consisting of SEQ ID NO:1-20. Themethod comprises a) culturing a cell under conditions suitable forexpression of the polypeptide, wherein said cell is transformed with arecombinant polynucleotide comprising a promoter sequence operablylinked to a polynucleotide encoding the polypeptide, and b) recoveringthe polypeptide so expressed.

[0057] Yet another embodiment provides an isolated antibody whichspecifically binds to a polypeptide selected from the group consistingof a) a polypeptide comprising an amino acid sequence selected from thegroup consisting of SEQ ID NO:1-20, b) a polypeptide comprising anaturally occurring amino acid sequence at least 90% identical or atleast about 90% identical to an amino acid sequence selected from thegroup consisting of SEQ ID NO:1-20, c) a biologically active fragment ofa polypeptide having an amino acid sequence selected from the groupconsisting of SEQ NO: 1-20, and d) an immunogenic fragment of apolypeptide having an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20.

[0058] Still yet another embodiment provides an isolated polynucleotideselected from the group consisting of a) a polynucleotide comprising apolynucleotide sequence selected from the group consisting of SEQ IDNO:21-40, b) a polynucleotide comprising a naturally occurringpolynucleotide sequence at least 90% identical or at least about 90%identical to a polynucleotide sequence selected from the groupconsisting of SEQ ID NO:21-40, c) a polynucleotide complementary to thepolynucleotide of a), d) a polynucleotide complementary to thepolynucleotide of b), and e) an RNA equivalent of a)-d). In otherembodiments, the polynucleotide can comprise at least about 20, 30, 40,60, 80, or 100 contiguous nucleotides.

[0059] Yet another embodiment provides a method for detecting a targetpolynucleotide in a sample, said target polynucleotide being selectedfrom the group consisting of a) a polynucleotide comprising apolynucleotide sequence selected from the group consisting of SEQ IDNO:21-40, b) a polynucleotide comprising a naturally occurringpolynucleotide sequence at least 90% identical or at least about 90%identical to a polynucleotide sequence selected from the groupconsisting of SEQ ID NO:21-40, c) a polynucleotide complementary to thepolynucleotide of a), d) a polynucleotide complementary to thepolynucleotide of b), and e) an RNA equivalent of a)-d). The methodcomprises a) hybridizing the sample with a probe comprising at least 20contiguous nucleotides comprising a sequence complementary to saidtarget polynucleotide in the sample, and which probe specificallyhybridizes to said target polynucleotide, under conditions whereby ahybridization complex is formed between said probe and said targetpolynucleotide or fragments thereof, and b) detecting the presence orabsence of said hybridization complex. In a related embodiment, themethod can include detecting the amount of the hybridization complex. Instill other embodiments, the probe can comprise at least about 20, 30,40, 60, 80, or 100 contiguous nucleotides.

[0060] Still yet another embodiment provides a method for detecting atarget polynucleotide in a sample, said target polynucleotide beingselected from the group consisting of a) a polynucleotide comprising apolynucleotide sequence selected from the group consisting of SEQ IDNO:21-40, b) a polynucleotide comprising a naturally occurringpolynucleotide sequence at least 90% identical or at least about 90%identical to a polynucleotide sequence selected from the groupconsisting of SEQ ID NO:21-40, c) a polynucleotide complementary to thepolynucleotide of a), d) a polynucleotide complementary to thepolynucleotide of b), and e) an RNA equivalent of a)-d). The methodcomprises a) amplifying said target polynucleotide or fragment thereofusing polymerase chain reaction amplification, and b) detecting thepresence or absence of said amplified target polynucleotide or fragmentthereof. In a related embodiment, the method can include detecting theamount of the amplified target polynucleotide or fragment thereof.

[0061] Another embodiment provides a composition comprising an effectiveamount of a polypeptide selected from the group consisting of a) apolypeptide comprising an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20, b) a polypeptide comprising a naturallyoccurring amino acid sequence at least 90% identical or at least about90% identical to an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20, c) a biologically active fragment of apolypeptide having an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20, and d) an immunogenic fragment of apolypeptide having an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20, and a pharmaceutically acceptableexcipient. In one embodiment, the composition can comprise an amino acidsequence selected from the group consisting of SEQ ID NO:1-20. Otherembodiments provide a method of treating a disease or conditionassociated with decreased or abnormal expression of functional VAP,comprising administering to a patient in need of such treatment thecomposition.

[0062] Yet another embodiment provides a method for screening a compoundfor effectiveness as an agonist of a polypeptide selected from the groupconsisting of a) a polypeptide comprising an amino acid sequenceselected from the group consisting of SEQ ID NO:1-20, b) a polypeptidecomprising a naturally occurring amino acid sequence at least 90%identical or at least about 90% identical to an amino acid sequenceselected from the group consisting of SEQ ID NO:1-20, c) a biologicallyactive fragment of a polypeptide having an amino acid sequence selectedfrom the group consisting of SEQ ID NO:1-20, and d) an immunogenicfragment of a polypeptide having an amino acid sequence selected fromthe group consisting of SEQ ID NO:1-20. The method comprises a) exposinga sample comprising the polypeptide to a compound, and b) detectingagonist activity in the sample. Another embodiment provides acomposition comprising an agonist compound identified by the method anda pharmaceutically acceptable excipient. Yet another embodiment providesa method of treating a disease or condition associated with decreasedexpression of functional VAP, comprising administering to a patient inneed of such treatment the composition.

[0063] Still yet another embodiment provides a method for screening acompound for effectiveness as an antagonist of a polypeptide selectedfrom the group consisting of a) a polypeptide comprising an amino acidsequence selected from the group consisting of SEQ ID NO:1-20, b) apolypeptide comprising a naturally occurring amino acid sequence atleast 90% identical or at least about 90% identical to an amino acidsequence selected from the group consisting of SEQ ID NO:1-20, c) abiologically active fragment of a polypeptide having an amino acidsequence selected from the group consisting of SEQ ID NO:1-20, and d) animmunogenic fragment of a polypeptide having an amino acid sequenceselected from the group consisting of SEQ ID NO:1-20. The methodcomprises a) exposing a sample comprising the polypeptide to a compound,and b) detecting antagonist activity in the sample. Another embodimentprovides a composition comprising an antagonist compound identified bythe method and a pharmaceutically acceptable excipient. Yet anotherembodiment provides a method of treating a disease or conditionassociated with overexpression of functional VAP, comprisingadministering to a patient in need of such treatment the composition.

[0064] Another embodiment provides a method of screening for a compoundthat specifically binds to a polypeptide selected from the groupconsisting of a) a polypeptide comprising an amino acid sequenceselected from the group consisting of SEQ ID NO:1-20, b) a polypeptidecomprising a naturally occurring amino acid sequence at least 90%identical or at least about 90% identical to an amino acid sequenceselected from the group consisting of SEQ ID NO:1-20, c) a biologicallyactive fragment of a polypeptide having an amino acid sequence selectedfrom the group consisting of SEQ ID NO:1-20, and d) an immunogenicfragment of a polypeptide having an amino acid sequence selected fromthe group consisting of SEQ ID NO:1-20. The method comprises a)combining the polypeptide with at least one test compound under suitableconditions, and b) detecting binding of the polypeptide to the testcompound, thereby identifying a compound that specifically binds to thepolypeptide.

[0065] Yet another embodiment provides a method of screening for acompound that modulates the activity of a polypeptide selected from thegroup consisting of a) a polypeptide comprising an amino acid sequenceselected from the group consisting of SEQ ID NO:1-20, b) a polypeptidecomprising a naturally occurring amino acid sequence at least 90%identical or at least about 90% identical to an amino acid sequenceselected from the group consisting of SEQ ID NO:1-20, c) a biologicallyactive fragment of a polypeptide having an amino acid sequence selectedfrom the group consisting of SEQ ID NO:1-20, and d) an immunogenicfragment of a polypeptide having an amino acid sequence selected fromthe group consisting of SEQ ID NO:1-20. The method comprises a)combining the polypeptide with at least one test compound underconditions permissive for the activity of the polypeptide, b) assessingthe activity of the polypeptide in the presence of the test compound,and c) comparing the activity of the polypeptide in the presence of thetest compound with the activity of the polypeptide in the absence of thetest compound, wherein a change in the activity of the polypeptide inthe presence of the test compound is indicative of a compound thatmodulates the activity of the polypeptide.

[0066] Still yet another embodiment provides a method for screening acompound for effectiveness in altering expression of a targetpolynucleotide, wherein said target polynucleotide comprises apolynucleotide sequence selected from the group consisting of SEQ IDNO:21-40, the method comprising a) exposing a sample comprising thetarget polynucleotide to a compound, b) detecting altered expression ofthe target polynucleotide, and c) comparing the expression of the targetpolynucleotide in the presence of varying amounts of the compound and inthe absence of the compound.

[0067] Another embodiment provides a method for assessing toxicity of atest compound, said method comprising a) treating a biological samplecontaining nucleic acids with the test compound; b) hybridizing thenucleic acids of the treated biological sample with a probe comprisingat least 20 contiguous nucleotides of a polynucleotide selected from thegroup consisting of i) a polynucleotide comprising a polynucleotidesequence selected from the group consisting of SEQ ID NO:21-40, ii) apolynucleotide comprising a naturally occurring polynucleotide sequenceat least 90% identical or at least about 90% identical to apolynucleotide sequence selected from the group consisting of SEQ IDNO:21-40, iii) a polynucleotide having a sequence complementary to i),iv) a polynucleotide complementary to the polynucleotide of ii), and v)an RNA equivalent of i)-iv). Hybridization occurs under conditionswhereby a specific hybridization complex is formed between said probeand a target polynucleotide in the biological sample, said targetpolynucleotide selected from the group consisting of i) a polynucleotidecomprising a polynucleotide sequence selected from the group consistingof SEQ ID NO:21140, ii) a polynucleotide comprising a naturallyoccurring polynucleotide sequence at least 90% identical or at leastabout 90% identical to a polynucleotide sequence selected from the groupconsisting of SEQ ID NO:21-40, iji) a polynucleotide complementary tothe polynucleotide of i), iv) a polynucleotide complementary to thepolynucleotide of ii), and v) an RNA equivalent of i)-iv).Alternatively, the target polynucleotide can comprise a fragment of apolynucleotide selected from the group consisting of i)-v) above; c)quantifying the amount of hybridization complex; and d) comparing theamount of hybridization complex in the treated biological sample withthe amount of hybridization complex in an untreated biological sample,wherein a difference in the amount of hybridization complex in thetreated biological sample is indicative of toxicity of the testcompound.

BRIEF DESCRIPTION OF THE TABLES

[0068] Table 1 summarizes the nomenclature for full lengthpolynucleotide and polypeptide embodiments of the invention.

[0069] Table 2 shows the GenBank identification number and annotation ofthe nearest GenBank homolog, and the PROTEOME database identificationnumbers and annotations of PROTEOME database homologs, for polypeptideembodiments of the invention. The probability scores for the matchesbetween each polypeptide and its homolog(s) are also shown.

[0070] Table 3 shows structural features of polypeptide embodiments,including predicted motifs and domains, along with the methods,algorithms, and searchable databases used for analysis of thepolypeptides.

[0071] Table 4 lists the cDNA and/or genomic DNA fragments which wereused to assemble polynucleotide embodiments, along with selectedfragments of the polynucleotides.

[0072] Table 5 shows representative cDNA libraries for polynucleotideembodiments.

[0073] Table 6 provides an appendix which describes the tissues andvectors used for construction of the cDNA libraries shown in Table 5.

[0074] Table 7 shows the tools, programs, and algorithms used to analyzepolynucleotides and polypeptides, along with applicable descriptions,references, and threshold parameters.

[0075] Table 8 shows single nucleotide polymorphisms found inpolynucleotide sequences of the invention, along with allele frequenciesin different human populations.

DESCRIPTION OF THE INVENTION

[0076] Before the present proteins, nucleic acids, and methods aredescribed, it is understood that embodiments of the invention are notlimited to the particular machines, instruments, materials, and methodsdescribed, as these may vary. It is also to be understood that theterminology used herein is for the purpose of describing particularembodiments only, and is not intended to limit the scope of theinvention.

[0077] As used herein and in the appended claims, the singular forms“a,” “an,” and “the” include plural reference unless the context clearlydictates otherwise. Thus, for example, a reference to “a host cell”includes a plurality of such host cells, and a reference to “anantibody” is a reference to one or more antibodies and equivalentsthereof known to those skilled in the art, and so forth.

[0078] Unless defined otherwise, all technical and scientific terms usedherein have the same meanings as commonly understood by one of ordinaryskill in the art to which this invention belongs. Although any machines,materials, and methods similar or equivalent to those described hereincan be used to practice or test the present invention, the preferredmachines, materials and methods are now described. All publicationsmentioned herein are cited for the purpose of describing and disclosingthe cell lines, protocols, reagents and vectors which are reported inthe publications and which might be used in connection with variousembodiments of the invention. Nothing herein is to be construed as anadmission that the invention is not entitled to antedate such disclosureby virtue of prior invention.

[0079] Definitions

[0080] “VAP” refers to the amino acid sequences of substantiallypurified VAP obtained from any species, particularly a mammalianspecies, including bovine, ovine, porcine, murine, equine, and human,and from any source, whether natural, synthetic, semi-synthetic, orrecombinant.

[0081] The term “agonist” refers to a molecule which intensifies ormimics the biological activity of VAP. Agonists may include proteins,nucleic acids, carbohydrates, small molecules, or any other compound orcomposition which modulates the activity of VAP either by directlyinteracting with VAP or by acting on components of the biologicalpathway in which VAP participates.

[0082] An “allelic variant” is an alternative form of the gene encodingVAP. Allelic variants may result from at least one mutation in thenucleic acid sequence and may result in altered mRNAs or in polypeptideswhose structure or function may or may not be altered. A gene may havenone, one, or many allelic variants of its naturally occurring form.Common mutational changes which give rise to allelic variants aregenerally ascribed to natural deletions, additions, or substitutions ofnucleotides. Each of these types of changes may occur alone, or incombination with the others, one or more times in a given sequence.

[0083] “Altered” nucleic acid sequences encoding VAP include thosesequences with deletions, insertions, or substitutions of differentnucleotides, resulting in a polypeptide the same as VAP or a polypeptidewith at least one functional characteristic of VAP. Included within thisdefinition are polymorphisms which may or may not be readily detectableusing a particular oligonucleotide probe of the polynucleotide encodingVAP, and improper or unexpected hybridization to allelic variants, witha locus other than the normal chromosomal locus for the polynucleotideencoding VAP. The encoded protein may also be “altered,” and may containdeletions, insertions, or substitutions of amino acid residues whichproduce a silent change and result in a functionally equivalent VAP.Deliberate amino acid substitutions may be made on the basis of one ormore similarities in polarity, charge, solubility, hydrophobicity,hydrophilicity, and/or the amphipathic nature of the residues, as longas the biological or immunological activity of VAP is retained. Forexample, negatively charged amino acids may include aspartic acid andglutamic acid, and positively charged amino acids may include lysine andarginine. Amino acids with uncharged polar side chains having similarhydrophilicity values may include: asparagine and glutamine; and serineand threonine. Amino acids with uncharged side chains having similarhydrophilicity values may include: leucine, isoleucine, and valine;glycine and alanine; and phenylalanine and tyrosine.

[0084] The terms “amino acid” and “amino acid sequence” can refer to anoligopeptide, a peptide, a polypeptide, or a protein sequence, or afragment of any of these, and to naturally occurring or syntheticmolecules. Where “amino acid sequence” is recited to refer to a sequenceof a naturally occurring protein molecule, “amino acid sequence” andlike terms are not meant to limit the amino acid sequence to thecomplete native amino acid sequence associated with the recited proteinmolecule.

[0085] “Amplification” relates to the production of additional copies ofa nucleic acid. Amplification may be carried out using polymerase chainreaction (PCR) technologies or other nucleic acid amplificationtechnologies well known in the art.

[0086] The term “antagonist” refers to a molecule which inhibits orattenuates the biological activity of VAP. Antagonists may includeproteins such as antibodies, anticalins, nucleic acids, carbohydrates,small molecules, or any other compound or composition which modulatesthe activity of VAP either by directly interacting with VAP or by actingon components of the biological pathway in which VAP participates.

[0087] The term “antibody” refers to intact immunoglobulin molecules aswell as to fragments thereof, such as Fab, F(ab′)₂, and Fv fragments,which are capable of binding an epitopic determinant. Antibodies thatbind VAP polypeptides can be prepared using intact polypeptides or usingfragments containing small peptides of interest as the immunizingantigen. The polypeptide or oligopeptide used to immunize an animal(e.g., a mouse, a rat, or a rabbit) can be derived from the translationof RNA, or synthesized chemically, and can be conjugated to a carrierprotein if desired. Commonly used carriers that are chemically coupledto peptides include bovine serum albumin, thyroglobulin, and keyholelimpet hemocyanin (KLH). The coupled peptide is then used to immunizethe animal.

[0088] The term “antigenic determinant” refers to that region of amolecule (i.e., an epitope) that makes contact with a particularantibody. When a protein or a fragment of a protein is used to immunizea host animal, numerous regions of the protein may induce the productionof antibodies which bind specifically to antigenic determinants(particular regions or three-dimensional structures on the protein). Anantigenic determinant may compete with the intact antigen (i.e., theimmunogen used to elicit the immune response) for binding to anantibody.

[0089] The term “aptamer” refers to a nucleic acid or oligonucleotidemolecule that binds to a specific molecular target. Aptamers are derivedfrom an in vitro evolutionary process (e.g., SELEX (Systematic Evolutionof Ligands by EXponential Enrichment), described in U.S. Pat. No.5,270,163), which selects for target-specific aptamer sequences fromlarge combinatorial libraries. Aptamer compositions may bedouble-stranded or single-stranded, and may includedeoxyribonucleotides, ribonucleotides, nucleotide derivatives, or othernucleotide-like molecules. The nucleotide components of an aptamer mayhave modified sugar groups (e.g., the 2′-OH group of a ribonucleotidemay be replaced by 2′-F or 2′-NH₂), which may improve a desiredproperty, e.g., resistance to nucleases or longer lifetime in blood.Aptamers may be conjugated to other molecules, e.g., a high molecularweight carrier to slow clearance of the aptamer from the circulatorysystem. Aptamers may be specifically cross-linked to their cognateligands, e.g., by photo-activation of a cross-linker (Brody, E. N. andL. Gold (2000) J. Biotechnol. 74:5-13).

[0090] The term “intramer” refers to an aptamer which is expressed invivo. For example, a vaccinia virus-based RNA expression system has beenused to express specific RNA aptamers at high levels in the cytoplasm ofleukocytes (Blind, M. et al. (1999) Proc. Natl. Acad. Sci. USA96:3606-3610).

[0091] The term “spiegelmer” refers to an aptamer which includes L-DNA,L-RNA, or other left-handed nucleotide derivatives or nucleotide-likemolecules. Aptamers containing left-handed nucleotides are resistant todegradation by naturally occurring enzymes, which normally act onsubstrates containing right-handed nucleotides.

[0092] The term “antisense” refers to any composition capable ofbase-pairing with the “sense” (coding) strand of a polynucleotide havinga specific nucleic acid sequence. Antisense compositions may includeDNA; RNA; peptide nucleic acid (PNA); oligonucleotides having modifiedbackbone linkages such as phosphorothioates, methylphosphonates, orbenzylphosphonates; oligonucleotides having modified sugar groups suchas 2′-methoxyethyl sugars or 2′-methoxyethoxy sugars; oroligonucleotides having modified bases such as 5-methyl cytosine,2′-deoxyuracil, or 7-deaza-2′-deoxyguanosine. Antisense molecules maybeproduced by any method including chemical synthesis or transcription.Once introduced into a cell, the complementary antisense moleculebase-pairs with a naturally occurring nucleic acid sequence produced bythe cell to form duplexes which block either transcription ortranslation. The designation “negative” or “minus” can refer to theantisense strand, and the designation “positive” or “plus” can refer tothe sense strand of a reference DNA molecule.

[0093] The term “biologically active” refers to a protein havingstructural, regulatory, or biochemical functions of a naturallyoccurring molecule. Likewise, “immunologically active” or “immunogenic”refers to the capability of the natural, recombinant, or synthetic VAP,or of any oligopeptide thereof, to induce a specific immune response inappropriate animals or cells and to bind with specific antibodies.

[0094] “Complementary” describes the relationship between twosingle-stranded nucleic acid sequences that anneal by base-pairing. Forexample, 5′-AGT-3′ pairs with its complement, 3′-TCA-5′.

[0095] A “composition comprising a given polynucleotide” and a“composition comprising a given polypeptide” can refer to anycomposition containing the given polynucleotide or polypeptide. Thecomposition may comprise a dry formulation or an aqueous solution.Compositions comprising polynucleotides encoding VAP or fragments of VAPmay be employed as hybridization probes. The probes may be stored infreezeried form and may be associated with a stabilizing agent such as acarbohydrate. In hybridizations, the probe may be deployed in an aqueoussolution containing salts (e.g., NaCl), detergents (e.g., sodium dodecylsulfate; SDS), and other components (e.g., Denhardt's solution, drymilk, salmon sperm DNA, etc.).

[0096] “Consensus sequence” refers to a nucleic acid sequence which hasbeen subjected to repeated DNA sequence analysis to resolve uncalledbases, extended using the XL-PCR kit (Applied Biosystems, Foster CityCalif.) in the 5′ and/or the 3′ direction, and resequenced, or which hasbeen assembled from one or more overlapping cDNA, EST, or genomic DNAfragments using a computer program for fragment assembly, such as theGELVIEW fragment assembly system (Accelrys, Burlington Mass.) or Phrap(University of Washington, Seattle Wash.). Some sequences have been bothextended and assembled to produce the consensus sequence.

[0097] “Conservative amino acid substitutions” are those substitutionsthat are predicted to least interfere with the properties of theoriginal protein, i.e., the structure and especially the function of theprotein is conserved and not significantly changed by suchsubstitutions. The table below shows amino acids which may besubstituted for an original amino acid in a protein and which areregarded as conservative amino acid substitutions. Original ResidueConservative Substitution Ala Gly, Ser Arg His, Lys Asn Asp, Gln, HisAsp Asn, Glu Cys Ala, Ser Gln Asn, Glu, His Glu Asp, Gln, His Gly AlaHis Asn, Arg, Gln, Glu Ile Leu, Val Leu Ile, Val Lys Arg, Gln, Glu MetLeu, Ile Phe His, Met, Leu, Trp, Tyr Ser Cys, Thr Thr Ser, Val Trp Phe,Tyr Tyr His, Phe, Trp Val Ile, Leu, Thr

[0098] Conservative amino acid substitutions generally maintain (a) thestructure of the polypeptide backbone in the area of the substitution,for example, as a beta sheet or alpha helical conformation, (b) thecharge or hydrophobicity of the molecule at the site of thesubstitution, and/or (c) the bulk of the side chain.

[0099] A “deletion” refers to a change in the amino acid or nucleotidesequence that results in the absence of one or more amino acid residuesor nucleotides.

[0100] The term “derivative” refers to a chemically modifiedpolynucleotide or polypeptide. Chemical modifications of apolynucleotide can include, for example, replacement of hydrogen by analkyl, acyl, hydroxyl, or amino group. A derivative polynucleotideencodes a polypeptide which retains at least one biological orimmunological function of the natural molecule. A derivative polypeptideis one modified by glycosylation, pegylation, or any similar processthat retains at least one biological or immunological function of thepolypeptide from which it was derived.

[0101] A “detectable label” refers to a reporter molecule or enzyme thatis capable of generating a measurable signal and is covalently ornoncovalently joined to a polynucleotide or polypeptide.

[0102] “Differential expression” refers to increased or upregulated; ordecreased, downregulated, or absent gene or protein expression,determined by comparing at least two different samples. Such comparisonsmay be carried out between, for example, a treated and an untreatedsample, or a diseased and a normal sample.

[0103] “Exon shuffling” refers to the recombination of different codingregions (exons). Since an exon may represent a structural or functionaldomain of the encoded protein, new proteins may be assembled through thenovel reassortment of stable substructures, thus allowing accelerationof the evolution of new protein functions.

[0104] A “fragment” is a unique portion of VAP or a polynucleotideencoding VAP which can be identical in sequence to, but shorter inlength than, the parent sequence. A fragment may comprise up to theentire length of the defined sequence, minus one nucleotide/amino acidresidue. For example, a fragment may comprise from about 5 to about 1000contiguous nucleotides or amino acid residues. A fragment used as aprobe, primer, antigen, therapeutic molecule, or for other purposes, maybe at least 5, 10, 15, 16, 20, 25, 30, 40, 50, 60, 75, 100, 150, 250 orat least 500 contiguous nucleotides or amino acid residues in length.Fragments may be preferentially selected from certain regions of amolecule. For example, a polypeptide fragment may comprise a certainlength of contiguous amino acids selected from the first 250 or 500amino acids (or first 25% or 50%) of a polypeptide as shown in a certaindefined sequence. Clearly these lengths are exemplary, and any lengththat is supported by the specification, including the Sequence Listing,tables, and figures, may be encompassed by the present embodiments.

[0105] A fragment of SEQ ID NO:21-40 can comprise a region of uniquepolynucleotide sequence that specifically identifies SEQ ID NO:21-40,for example, as distinct from any other sequence in the genome fromwhich the fragment was obtained. A fragment of SEQ ID NO:21-40 can beemployed in one or more embodiments of methods of the invention, forexample, in hybridization and amplification technologies and inanalogous methods that distinguish SEQ ID NO:21-40 from relatedpolynucleotides. The precise length of a fragment of SEQ ID NO:21-40 andthe region of SEQ ID NO:21-40 to which the fragment corresponds areroutinely determinable by one of ordinary skill in the art based on theintended purpose for the fragment.

[0106] A fragment of SEQ ID NO:1-20 is encoded by a fragment of SEQ IDNO:21-40. A fragment of SEQ ID NO:1-20 can comprise a region of uniqueamino acid sequence that specifically identifies SEQ ID NO:1-20. Forexample, a fragment of SEQ ID NO:1-20 can be used as an immunogenicpeptide for the development of antibodies that specifically recognizeSEQ ID NO:1-20. The precise length of a fragment of SEQ ID NO:1-20 andthe region of SEQ ID NO:1-20 to which the fragment corresponds can bedetermined based on the intended purpose for the fragment using one ormore analytical methods described herein or otherwise known in the art.

[0107] A “full length” polynucleotide is one containing at least atranslation initiation codon (e.g., methionine) followed by an openreading frame and a translation termination codon. A “full length”polynucleotide sequence encodes a “full length” polypeptide sequence.

[0108] “Homology” refers to sequence similarity or, alternatively,sequence identity, between two or more polynucleotide sequences or twoor more polypeptide sequences.

[0109] The terms “percent identity” and “% identity,” as applied topolynucleotide sequences, refer to the percentage of identical residuematches between at least two polynucleotide sequences aligned using astandardized algorithm. Such an algorithm may insert, in a standardizedand reproducible way, gaps in the sequences being compared in order tooptimize alignment between two sequences, and therefore achieve a moremeaningful comparison of the two sequences.

[0110] Percent identity between polynucleotide sequences may bedetermined using one or more computer algorithms or programs known inthe art or described herein. For example, percent identity can bedetermined using the default parameters of the CLUSTAL V algorithm asincorporated into the MEGALIGN version 3.12e sequence alignment program.This program is part of the LASERGENE software package, a suite ofmolecular biological analysis programs (DNASTAR, Madison Wis.). CLUSTALV is described in Higgins, D. G. and P. M. Sharp (1989; CABIOS5:151-153) and in Higgins, D. G. et al. (1992; CABIOS 8:189-191). Forpairwise alignments of polynucleotide sequences, the default parametersare set as follows: Ktuple=2, gap penalty=5, window=4, and “diagonalssaved”=4. The “weighted” residue weight table is selected as thedefault.

[0111] Alternatively, a suite of commonly used and freely availablesequence comparison algorithms which can be used is provided by theNational Center for Biotechnology Information (NCBI) Basic LocalAlignment Search Tool (BLAST) (Altschul, S. F. et al. (1990) J. Mol.Biol. 215:403-410), which is available from several sources, includingthe NCBI, Bethesda, Md., and on the Internet athttp://www.ncbi.nlm.nih.gov/BLASTV. The BLAST software suite includesvarious sequence analysis programs including “blastn,” that is used toalign a known polynucleotide sequence with other polynucleotidesequences from a variety of databases. Also available is a tool called“BLAST 2 Sequences” that is used for direct pairwise comparison of twonucleotide sequences. “BLAST 2 Sequences” can be accessed and usedinteractively at http://www.ncbi.nlm.nih.gov/gorf/bl2.html. The “BLAST 2Sequences” tool can be used for both blastn and blastp (discussedbelow). BLAST programs are commonly used with gap and other parametersset to default settings. For example, to compare two nucleotidesequences, one may use blastn with the “BLAST 2 Sequences” tool Version2.0.12 (April-21-2000) set at default parameters. Such defaultparameters may be, for example:

[0112] Matrix: BLOSUM62

[0113] Rewardfor matchl: 1

[0114] Penalty for mismatch: −2

[0115] Open Gap: 5 and Extension Gap: 2 penalties

[0116] Gap×drop-off. 50

[0117] Expect: 10

[0118] Word Size: 11

[0119] Filter: on

[0120] Percent identity may be measured over the length of an entiredefined sequence, for example, as defined by a particular SEQ ID number,or may be measured over a shorter length, for example, over the lengthof a fragment taken from a larger, defined sequence, for instance, afragment of at least 20, at least 30, at least 40, at least 50, at least70, at least 100, or at least 200 contiguous nucleotides. Such lengthsare exemplary only, and it is understood that any fragment lengthsupported by the sequences shown herein, in the tables, figures, orSequence Listing, may be used to describe a length over which percentageidentity may be measured.

[0121] Nucleic acid sequences that do not show a high degree of identitymay nevertheless encode similar amino acid sequences due to thedegeneracy of the genetic code. It is understood that changes in anucleic acid sequence can be made using this degeneracy to producemultiple nucleic acid sequences that all encode substantially the sameprotein.

[0122] The phrases “percent identity” and “% identity,” as applied topolypeptide sequences, refer to the percentage of identical residuematches between at least two polypeptide sequences aligned using astandardized algorithm. Methods of polypeptide sequence alignment arewell-known. Some alignment methods take into account conservative aminoacid substitutions. Such conservative substitutions, explained in moredetail above, generally preserve the charge and hydrophobicity at thesite of substitution, thus preserving the structure (and thereforefunction) of the polypeptide. The phrases “percent similarity” and “%similarity,” as applied to polypeptide sequences, refer to thepercentage of residue matches, including identical residue matches andconservative substitutions, between at least two polypeptide sequencesaligned using a standardized algorithm. In contrast, conservativesubstitutions are not included in the calculation of percent identitybetween polypeptide sequences.

[0123] Percent identity between polypeptide sequences may be determinedusing the default parameters of the CLUSTAL V algorithm as incorporatedinto the MEGALIGN version 3.12e sequence alignment program (describedand referenced above). For pairwise alignments of polypeptide sequencesusing CLUSTAL V, the default parameters are set as follows: Ktuple=1,gap penalty=3, window=5, and “diagonals saved”=5. The PAM250 matrix isselected as the default residue weight table.

[0124] Alternatively the NCBI BLAST software suite may be used. Forexample, for a pairwise comparison of two polypeptide sequences, one mayuse the “BLAST 2 Sequences” tool Version 2.0.12 (April-21-2000) withblastp set at default parameters. Such default parameters may be, forexample:

[0125] Matrix: BLOSUM62

[0126] Open Gap: 11 and Extension Gap: 1 penalties

[0127] Gap×drop-off. 50

[0128] Expect: 10

[0129] Word Size: 3

[0130] Filter: on

[0131] Percent identity may be measured over the length of an entiredefined polypeptide sequence, for example, as defined by a particularSEQ ID number, or may be measured over a shorter length, for example,over the length of a fragment taken from a larger, defined polypeptidesequence, for instance, a fragment of at least 15, at least 20, at least30, at least 40, at least 50, at least 70 or at least 150 contiguousresidues. Such lengths are exemplary only, and it is understood that anyfragment length supported by the sequences shown herein, in the tables,figures or Sequence Listing, may be used to describe a length over whichpercentage identity may be measured.

[0132] “Human artificial chromosomes” (HACs) are linear microchromosomeswhich may contain DNA sequences of about 6 kb to 10 Mb in size and whichcontain all of the elements required for chromosome replication,segregation and maintenance.

[0133] The term “humanized antibody” refers to an antibody molecule inwhich the amino acid sequence in the non-antigen binding regions hasbeen altered so that the antibody more closely resembles a humanantibody, and still retains its original binding ability.

[0134] “Hybridization” refers to the process by which a polynucleotidestrand anneals with a complementary strand through base pairing underdefined hybridization conditions. Specific hybridization is anindication that two nucleic acid sequences share a high degree ofcomplementarity. Specific hybridization complexes form under permissiveannealing conditions and remain hybridized after the “washing” step(s).The washing step(s) is particularly important in determining thestringency of the hybridization process, with more stringent conditionsallowing less non-specific binding, i.e., binding between pairs ofnucleic acid strands that are not perfectly matched. Permissiveconditions for annealing of nucleic acid sequences are routinelydeterminable by one of ordinary skill in the art and may be consistentamong hybridization experiments, whereas wash conditions may be variedamong experiments to achieve the desired stringency, and thereforehybridization specificity. Permissive annealing conditions occur, forexample, at 68° C. in the presence of about 6×SSC, about 1% (w/v) SDS,and about 100 μg/ml sheared, denatured salmon sperm DNA.

[0135] Generally, stringency of hybridization is expressed, in part,with reference to the temperature under which the wash step is carriedout. Such wash temperatures are typically selected to be about 5° C. to20° C. lower than the thermal melting point (T_(m)) for the specificsequence at a defined ionic strength and pH. The T_(m) is thetemperature (under defined ionic strength and pH) at which 50% of thetarget sequence hybridizes to a perfectly matched probe. An equation forcalculating T_(m) and conditions for nucleic acid hybridization are wellknown and can be found in Sambrook, J. and D. W. Russell (2001;Molecular Cloning: A Laboratory Manual, 3rd ed., vol. 1-3, Cold SpringHarbor Press, Cold Spring Harbor N.Y., ch. 9).

[0136] High stringency conditions for hybridization betweenpolynucleotides of the present invention include wash conditions of 68°C. in the presence of about 0.2×SSC and about 0.1% SDS, for 1 hour.Alternatively, temperatures of about 65° C., 60° C., 55° C., or 42° C.may be used. SSC concentration may be varied from about 0.1 to 2×SSC,with SDS being present at about 0.1%. Typically, blocking reagents areused to block non-specific hybridization. Such blocking reagentsinclude, for instance, sheared and denatured salmon sperm DNA at about100-200 μg/ml. Organic solvent, such as formamide at a concentration ofabout 35-50% v/v, may also be used under particular circumstances, suchas for RNA:DNA hybridizations. Useful variations on these washconditions will be readily apparent to those of ordinary skill in theart. Hybridization, particularly under high stringency conditions, maybe suggestive of evolutionary similarity between the nucleotides. Suchsimilarity is strongly indicative of a similar role for the nucleotidesand their encoded polypeptides.

[0137] The term “hybridization complex” refers to a complex formedbetween two nucleic acids by virtue of the formation of hydrogen bondsbetween complementary bases. A hybridization complex may be formed insolution (e.g., Cot or Rot analysis) or formed between one nucleic acidpresent in solution and another nucleic acid immobilized on a solidsupport (e.g., paper, membranes, filters, chips, pins or glass slides,or any other appropriate substrate to which cells or their nucleic acidshave been fixed).

[0138] The words “insertion” and “addition” refer to changes in an aminoacid or polynucleotide sequence resulting in the addition of one or moreamino acid residues or nucleotides, respectively.

[0139] “Immune response” can refer to conditions associated withinflammation, trauma, immune disorders, or infectious or geneticdisease, etc. These conditions can be characterized by expression ofvarious factors, e.g., cytokines, chemokines, and other signalingmolecules, which may affect cellular and systemic defense systems.

[0140] An “immunogenic fragment” is a polypeptide or oligopeptidefragment of VAP which is capable of eliciting an immune response whenintroduced into a living organism, for example, a mammal. The term“immunogenic fragment” also includes any polypeptide or oligopeptidefragment of VAP which is useful in any of the antibody productionmethods disclosed herein or known in the art.

[0141] The term “microarray” refers to an arrangement of a plurality ofpolynucleotides, polypeptides, antibodies, or other chemical compoundson a substrate.

[0142] The terms “element” and “array element” refer to apolynucleotide, polypeptide, antibody, or other chemical compound havinga unique and defined position on a microarray.

[0143] The term “modulate” refers to a change in the activity of VAP.For example, modulation may cause an increase or a decrease in proteinactivity, binding characteristics, or any other biological, functional,or immunological properties of VAP.

[0144] The phrases “nucleic acid” and “nucleic acid sequence” refer to anucleotide, oligonucleotide, polynucleotide, or any fragment thereof.These phrases also refer to DNA or RNA of genomic or synthetic originwhich may be single-stranded or double-stranded and may represent thesense or the antisense strand, to peptide nucleic acid (PNA), or to anyDNA-like or RNA-like material.

[0145] “Operably linked” refers to the situation in which a firstnucleic acid sequence is placed in a functional relationship with asecond nucleic acid sequence. For instance, a promoter is operablylinked to a coding sequence if the promoter affects the transcription orexpression of the coding sequence. Operably linked DNA sequences may bein close proximity or contiguous and, where necessary to join twoprotein coding regions, in the same reading frame.

[0146] “Peptide nucleic acid” (PNA) refers to an antisense molecule oranti-gene agent which comprises an oligonucleotide of at least about 5nucleotides in length linked to a peptide backbone of amino acidresidues ending in lysine. The terminal lysine confers solubility to thecomposition. PNAs preferentially bind complementary single stranded DNAor RNA and stop transcript elongation, and may be pegylated to extendtheir lifespan in the cell.

[0147] “Post-translational modification” of an VAP may involvelipidation, glycosylation, phosphorylation, acetylation, racemization,proteolytic cleavage, and other modifications known in the art. Theseprocesses may occur synthetically or biochemically. Biochemicalmodifications will ary by cell type depending on the enzymatic milieu ofVAP.

[0148] “Probe” refers to nucleic acids encoding VAP, their complements,or fragments thereof, which are used to detect identical, allelic orrelated nucleic acids. Probes are isolated oligonucleotides orpolynucleotides attached to a detectable label or reporter molecule.Typical labels include radioactive isotopes, ligands, chemiluminescentagents, and enzymes. “Primers” are short nucleic acids, usually DNAoligonucleotides, which may be annealed to a target polynucleotide bycomplementary base-pairing. The primer may then be extended along thetarget DNA strand by a DNA polymerase enzyme. Primer pairs can be usedfor amplification (and identification) of a nucleic acid, e.g., by thepolymerase chain reaction (PCR).

[0149] Probes and primers as used in the present invention typicallycomprise at least 15 contiguous nucleotides of a known sequence. Inorder to enhance specificity, longer probes and primers may also beemployed, such as probes and primers that comprise at least 20, 25, 30,40, 50, 60, 70, 80, 90, 100, or at least 150 consecutive nucleotides ofthe disclosed nucleic acid sequences. Probes and primers may beconsiderably longer than these examples, and it is understood that anylength supported by the specification, including the tables, figures,and Sequence Listing, may be used.

[0150] Methods for preparing and using probes and primers are describedin, for example, Sambrook, J. and D. W. Russell (2001; MolecularCloning: A Laboratory Manual, 3rd ed., vol. 1-3, Cold Spring HarborPress, Cold Spring Harbor N.Y.), Ausubel, F. M. et al. (1999; ShortProtocols in Molecular Biology, 4^(th) ed., John Wiley & Sons, New YorkN.Y.), and Innis, M. et al. (1990; PCR Protocols, A Guide to Methods andApplications, Academic Press, San Diego Calif.). PCR primer pairs can bederived from a known sequence, for example, by using computer programsintended for that purpose such as Primer (Version 0.5, 1991, WhiteheadInstitute for Biomedical Research, Cambridge Mass.).

[0151] Oligonucleotides for use as primers are selected using softwareknown in the art for such purpose. For example, OLIGO 4.06 software isuseful for the selection of PCR primer pairs of up to 100 nucleotideseach, and for the analysis of oligonucleotides and largerpolynucleotides of up to 5,000 nucleotides from an input polynucleotidesequence of up to 32 kilobases. Similar primer selection programs haveincorporated additional features for expanded capabilities. For example,the PrimOU primer selection program (available to the public from theGenome Center at University of Texas South West Medical Center, DallasTex.) is capable of choosing specific primers from megabase sequencesand is thus useful for designing primers on a genome-wide scope. ThePrimer3 primer selection program (available to the public from theWhitehead Institute/MI Center for Genome Research, Cambridge Mass.)allows the user to input a “mispriming library,” in which sequences toavoid as primer binding sites are user-specified. Primer3 is useful, inparticular, for the election of oligonucleotides for microarrays. (Thesource code for the latter two primer selection rograms may also beobtained from their respective sources and modified to meet the user'sspecific eeds.) The PrimeGen program (available to the public from theUK Human Genome Mapping roject Resource Centre, Cambridge UK) designsprimers based on multiple sequence alignments, thereby allowingselection of primers that hybridize to either the most conserved orleast conserved regions of aligned nucleic acid sequences. Hence, thisprogram is useful for identification of both unique and conservedoligonucleotides and polynucleotide fragments. The oligonucleotides andpolynucleotide fragments identified by any of the above selectionmethods are useful in hybridization technologies, for example, as PCR orsequencing primers, microarray elements, or specific probes to identifyfully or partially complementary polynucleotides in a sample of nucleicacids. Methods of oligonucleotide selection are not limited to thosedescribed above.

[0152] A “recombinant nucleic acid” is a nucleic acid that is notnaturally occurring or has a sequence that is made by an artificialcombination of two or more otherwise separated segments of sequence.This artificial combination is often accomplished by chemical synthesisor, more commonly, by the artificial manipulation of isolated segmentsof nucleic acids, e.g., by genetic engineering techniques such as thosedescribed in Sambrook and Russell (supra). The term recombinant includesnucleic acids that have been altered solely by addition, substitution,or deletion of a portion of the nucleic acid. Frequently, a recombinantnucleic acid may include a nucleic acid sequence operably linked to apromoter sequence. Such a recombinant nucleic acid may be part of avector that is used, for example, to transform a cell.

[0153] Alternatively, such recombinant nucleic acids may be part of aviral vector, e.g., based on a vaccinia virus, that could be use tovaccinate a mammal wherein the recombinant nucleic acid is expressed,inducing a protective immunological response in the mammal.

[0154] A “regulatory element” refers to a nucleic acid sequence usuallyderived from untranslated regions of a gene and includes enhancers,promoters, introns, and 5′ and 3′ untranslated regions (UTRs).Regulatory elements interact with host or viral proteins which controltranscription, translation, or RNA stability.

[0155] “Reporter molecules” are chemical or biochemical moieties usedfor labeling a nucleic acid, amino acid, or antibody. Reporter moleculesinclude radionuclides; enzymes; fluorescent, chemiluminescent, orchromogenic agents; substrates; cofactors; inhibitors; magneticparticles; and other moieties known in the art.

[0156] An “RNA equivalent,” in reference to a DNA molecule, is composedof the same linear sequence of nucleotides as the reference DNA moleculewith the exception that all occurrences of the nitrogenous base thymineare replaced with uracil, and the sugar backbone is composed of riboseinstead of deoxyribose.

[0157] The term “sample” is used in its broadest sense. A samplesuspected of containing VAP, nucleic acids encoding VAP, or fragmentsthereof may comprise a bodily fluid; an extract from a cell, chromosome,organelle, or membrane isolated from a cell; a cell; genomic DNA, RNA,or cDNA, in solution or bound to a substrate; a tissue; a tissue print;etc.

[0158] The terms “specific binding” and “specifically binding” refer tothat interaction between a protein or peptide and an agonist, anantibody, an antagonist, a small molecule, or any natural or syntheticbinding composition. The interaction is dependent upon the presence of aparticular structure of the protein, e.g., the antigenic determinant orepitope, recognized by the binding molecule. For example, if an antibodyis specific for epitope “A,” the presence of a polypeptide comprisingthe epitope A, or the presence of free unlabeled A, in a reactioncontaining free labeled A and the antibody will reduce the amount oflabeled A that binds to the antibody.

[0159] The term “substantially purified” refers to nucleic acid or aminoacid sequences that are removed from their natural environment and areisolated or separated, and are at least about 60% free, preferably atleast about 75% free, and most preferably at least about 90% free fromother components with which they are naturally associated.

[0160] A “substitution” refers to the replacement of one or more aminoacid residues or nucleotides by different amino acid residues ornucleotides, respectively.

[0161] “Substrate” refers to any suitable rigid or semi-rigid supportincluding membranes, filters, chips, slides, wafers, fibers, magnetic ornonmagnetic beads, gels, tubing, plates, polymers, microparticles andcapillaries. The substrate can have a variety of surface forms, such aswells, trenches, pins, channels and pores, to which polynucleotides orpolypeptides are bound.

[0162] A “transcript image” or “expression profile” refers to thecollective pattern of gene expression by a particular cell type ortissue under given conditions at a given time.

[0163] “Transformation” describes a process by which exogenous DNA isintroduced into a recipient cell. Transformation may occur under naturalor artificial conditions according to various methods well known in theart, and may rely on any known method for the insertion of foreignnucleic acid sequences into a prokaryotic or eukaryotic host cell. Themethod for transformation is selected based on the type of host cellbeing transformed and may include, but is not limited to, bacteriophageor viral infection, electroporation, heat shock, lipofection, andparticle bombardment. The term “transformed cells” includes stablytransformed cells in which the inserted DNA is capable of replicationeither as an autonomously replicating plasmid or as part of the hostchromosome, as well as transiently transformed cells which express theinserted DNA or RNA for limited periods of time.

[0164] A “transgenic organism,” as used herein, is any organism,including but not limited to animals and plants, in which one or more ofthe cells of the organism contains heterologous nucleic acid introducedby way of human intervention, such as by transgenic techniques wellknown in the art. The nucleic acid is introduced into the cell, directlyor indirectly by introduction into a precursor of the cell, by way ofdeliberate genetic manipulation, such as by microinjection or byinfection with a recombinant virus. In another embodiment, the nucleicacid can be introduced by infection with a recombinant viral vector,such as a lentiviral vector (Lois, C. et al. (2002) Science295:868-872). The term genetic manipulation does not include classicalcross-breeding, or in vitro fertilization, but rather is directed to theintroduction of a recombinant DNA molecule. The transgenic organismscontemplated in accordance with the present invention include bacteria,cyanobacteria, fungi, plants and animals. The isolated DNA of thepresent invention can be introduced into the host by methods known inthe art, for example infection, transfection, transformation ortransconjugation. Techniques for transferring the DNA of the presentinvention into such organisms are widely known and provided inreferences such as Sambrook and Russell (supra).

[0165] A “variant” of a particular nucleic acid sequence is defined as aniucleic acid sequence having at least 40% sequence identity to theparticular nucleic acid sequence over a certain length of one of thenucleic acid sequences using blastn with the “BLAST 2 Sequences” toolVersion 2.0.9 (May-07-1999) set at default parameters. Such a pair ofnucleic acids may show, for example, at least 50%, at least 60%, atleast 70%, at least 80%, at least 85%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, or at least 99% or greater sequence identityover a certain defined length. A variant may be described as, forexample, an “allelic” (as defined above), “splice,” “species,” or“polymorphic” variant. A splice variant may have significant identity toa reference molecule, but will generally have a greater or lesser numberof polynucleotides due to alternate splicing of exons during mRNAprocessing. The corresponding polypeptide may possess additionalfunctional domains or lack domains that are present in the referencemolecule. Species variants are polynucleotides that vary from onespecies to another. The resulting polypeptides will generally havesignificant amino acid identity relative to each other. A polymorphicvariant is a variation in the polynucleotide sequence of a particulargene between individuals of a given species. Polymorphic variants alsomay encompass “single nucleotide polymorphisms” (SNPs) in which thepolynucleotide sequence varies by one nucleotide base. The presence ofSNPs may be indicative of, for example, a certain population, a diseasestate, or a propensity for a disease state.

[0166] A “variant” of a particular polypeptide sequence is defined as apolypeptide sequence having at least 40% sequence identity or sequencesimilarity to the particular polypeptide sequence over a certain lengthof one of the polypeptide sequences using blastp with the “BLAST 2Sequences” tool Version 2.0.9 (May-07-1999) set at default parameters.Such a pair of polypeptides may show, for example, at least 50%, atleast 60%, at least 70%, at least 80%, at least 85%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% or greatersequence identity or sequence similarity over a certain defined lengthof one of the polypeptides.

[0167] The Invention

[0168] Various embodiments of the invention include new humanvesicle-associated proteins (VAP), the polynucleotides encoding VAP, andthe use of these compositions for the diagnosis, treatment, orprevention of vesicle trafficking disorders, autoimmune/inflammatorydisorders, and cancer.

[0169] Table 1 summarizes the nomenclature for the full lengthpolynucleotide and polypeptide embodiments of the invention. Eachpolynucleotide and its corresponding polypeptide are correlated to asingle Incyte project identification number (Incyte Project ID). Eachpolypeptide sequence is denoted by both a polypeptide sequenceidentification number (Polypeptide SEQ ID NO:) and an Incyte polypeptidesequence number (Incyte Polypeptide ID) as shown. Each polynucleotidesequence is denoted by both a polynucleotide sequence identificationnumber (Polynucleotide SEQ ID NO:) and an Incyte polynucleotideconsensus sequence number (Incyte Polynucleotide ID) as shown. Column 6shows the Incyte ID numbers of physical, full length clonescorresponding to the polypeptide and polynucleotide sequences of theinvention. The full length clones encode polypeptides which have atleast 95% sequence identity to the polypeptide sequences shown in column3.

[0170] Table 2 shows sequences with homology to polypeptide embodimentsof the invention as identified by BLAST analysis against the GenBankprotein (genpept) database and the PROTEOME database. Columns 1 and 2show the polypeptide sequence identification number (Polypeptide SEQ IDNO:) and the corresponding licyte polypeptide sequence number (IncytePolypeptide ID) for polypeptides of the invention. Column 3 shows theGenBank identification number (GenBank ID NO:) of the nearest GenBankhomolog and the PROTEOME database identification numbers (PROTEOME IDNO:) of the nearest PROTEOME database homologs. Column 4 shows theprobability scores for the matches between each polypeptide and itshomolog(s). Column 5 shows the annotation of the GenBank and PROTEOMEdatabase homolog(s) along with relevant citations where applicable, allof which are expressly incorporated by reference herein.

[0171] Table 3 shows various structural features of the polypeptides ofthe invention. Columns 1 and 2 show the polypeptide sequenceidentification number (SEQ ID NO:) and the corresponding Incytepolypeptide sequence number (Incyte Polypeptide ID) for each polypeptideof the invention. Column 3 shows the number of amino acid residues ineach polypeptide. Column 4 shows potential phosphorylation sites, andcolumn 5 shows potential glycosylation sites, as determined by theMOTIFS program of the GCG sequence analysis software package (Accelrys,Burlington Mass.). Column 6 shows amino acid residues comprisingsignature sequences, domains, and motifs. Column 7 shows analyticalmethods for protein structure/function analysis and in some cases,searchable databases to which the analytical methods were applied.

[0172] Together, Tables 2 and 3 sumnarize the properties of polypeptidesof the invention, and these properties establish that the claimedpolypeptides are vesicle-associated proteins. For example, SEQ ID NO:1is 31% identical, from residue V2 to residue P272, to human Golgimembrane protein GP73 (GenBank ID g7271867) as determined by the BasicLocal Alignment Search Tool (BLAST). (See Table 2.) The BLASTprobability score is 9.4e-26, which indicates the probability ofobtaining the observed polypeptide sequence alignment by chance. Datafrom TMHMMER analysis provides further corroborative evidence that SEQID NO:1 is a membrane protein localized to the Golgi apparatus. Inanother example, SEQ ID NO:3 is 99% identical, from residue M1 toresidue D744, to human N-ethylraleimide-sensitive factor (GenBank IDg7920147) as determined by the Basic Local Alignment Search Tool(BLAST). (See Table 2.) The BLAST probability score is 0.0, whichindicates the probability of obtaining the observed polypeptide sequencealignment by chance. SEQ ID NO:3 is localized to the subcellular region,has ATPase function, and has an AAA-protein family signature domain, asdetermined by BLAST analysis using the PROTEOME database. SEQ ID NO:3also contains an ATPase family associated with various cellularactivities (AAA) domain as determined by searching for statisticallysignificant matches in the hidden Markov model (H)-based PFAM databaseof conserved protein family domains. (See Table 3.) Data from BLIMPS,MOTIFS, PROHESCAN, and additional BLAST analyses provide furthercorroborative evidence that SEQ ID NO:3 is a vesicular protein of theAAA family. In another example, SEQ ID NO:9 is 100% identical, fromresidue F2 to residue E92, to rat clathrin-associated protein 17(GenBank ID g202928) as determined by the Basic Local Alignment SearchTool (BLAST). (See Table 2.) The BLAST probability score is 6.4E-45,which indicates the probability of obtaining the observed polypeptidesequence alignment by chance. SEQ ID NO:9 also has homology to humanadaptor-related protein complex 2 sigma 1 subunit which is associatedwith clathrin coated vesicles and is involved in intracellulartransport, as determined by BLAST analysis using the PROTEOME database.SEQ ID NO:9 also contains a clathrin adaptor complex small chain domainas determined by searching for statistically significant matches in thehidden Markov model (M)-based PFAM database of conserved protein familydomains. (See Table 3.) Data from PROFILESCAN, MOTIFS, and additionalBLAST analyses provide further corroborative evidence that SEQ ID NO:9is a clathrin-associated protein. In another example, SEQ ID NO:10 is95% identical, from residue M1 to residue M610, to rat clathrin assemblyprotein short form (GenBank ID g2792500) as determined by the BasicLocal Alignment Search Tool (BLAST). (See Table 2.) The BLASTprobability score is 0.0, which indicates the probability of obtainingthe observed polypeptide sequence alignment by chance. As determined byBLAST analysis using the PROTEOME database, SEQ ID NO:10 also hashomology to human and rat clathrin assembly lymphoid myeloid leukemiaproteins which bind to clathrin heavy chain (CLTC) and play a role incoated pit internalization. Rearrangements in the corresponding lymphoidmyeloid leukemia genes are associated with acute lymphoblastic and acutemyeloid leukemias (PROTEOME IDs 2984951PICALM and 3335201Rn.10888). SEQID NO:10 also contains an ENTH (Epsin N-terminal homology) domain (adomain found in proteins involved in endocytosis and cytoskeletalmachinery) as determined by searching for statistically significantmatches in the hidden Markov model (HMM)-based PFAM database ofconserved protein family domains. (See Table 3.) Data from additionalBLAST and MOTIFS analyses provide further corroborative evidence thatSEQ ID NO:10 is a clathrin assembly protein. In another example, SEQ IDNO:20 is 84% identical, from residue E17 to residue G262, to humansyntaxin 4A (placental) (GenBank ID g12803245) as determined by theBasic Local Alignrment Search Tool (BLAST). (See Table 2.) The BLASTprobability score is 2.6e-100, which indicates the probability ofobtaining the observed polypeptide sequence alignment by chance. SEQ IDNO:20 also has homology to proteins that are localized to the cytoplasm,have SNAP receptor (t-SNARE) function, and are syntaxins, as determinedby BLAST analysis using the PROTEOME database. SEQ ID NO:20 alsocontains a syntaxin domain, as determined by searching for statisticallysignificant matches in the hidden Markov model (HMM)-based PFAM databaseof conserved protein family domains, and contains a SMRT t SNARE domain(helical region found in SNARES) and a SMRT_SynN domain as determined bysearching for statistically significant matches in the hidden Markovmodel (HMM)-based SMRT database of conserved protein family domains.(See Table 3.) Data from BLIMPS, MOTIFS, and additional BLAST analysesprovide further corroborative evidence that SEQ ID NO:20 is a syntaxin.SEQ ID NO:2, SEQ ID NO:4-8, and SEQ ID NO:11-19 were analyzed andannotated in a similar manner. The algorithms and parameters for theanalysis of SEQ ID NO:1-20 are described in Table 7.

[0173] As shown in Table 4, the full length polynucleotide embodimentswere assembled using cDNA sequences or coding (exon) sequences derivedfrom genomic DNA, or any combination of these two types of sequences.Column 1 lists the polynucleotide sequence identification number(Polynucleotide SEQ ID NO:), the corresponding Incyte polynucleotideconsensus sequence number (Incyte ID) for each polynucleotide of theinvention, and the length of each polynucleotide sequence in basepairs.Column 2 shows the nucleotide start (5′) and stop (3′) positions of thecDNA and/or genomic sequences used to assemble the full lengthpolynucleotide embodiments, and of fragments of the polynucleotideswhich are useful, for example, in hybridization or amplificationtechnologies that identify SEQ ID NO:21-40 or that distinguish betweenSEQ ID NO:21-40 and related polynucleotides.

[0174] The polynucleotide fragments described in Column 2 of Table 4 mayrefer specifically, for example, to Incyte cDNAs derived fromtissue-specific cDNA libraries or from pooled cDNA libraries.Alternatively, the polynucleotide fragments described in column 2 mayrefer to GenBank cDNAs or ESTs which contributed to the assembly of thefull length polynucleotides. In addition, the polynucleotide fragmentsdescribed in column 2 may identify sequences derived from the ENSEMBL(The Sanger Centre, Cambridge, UK) database (i.e., those sequencesincluding the designation “ENST”). Alternatively, the polynucleotidefragments described in column 2 may be derived from the NCBI RefSeqNucleotide Sequence Records Database (i.e., those sequences includingthe designation “NM” or “NT”) or the NCBI RefSeq Protein SequenceRecords (i.e., those sequences including the designation “NP”).Alternatively, the polynucleotide fragments described in column 2 mayrefer to assemblages of both cDNA and Genscan-predicted exons broughttogether by an “exon stitching” algorithm. For example, a polynucleotidesequence identified as FL_XXXXXX_N_(1—)N_(2—)YYYYY_N_(3—)N₄ represents a“stitched” sequence in which XXXXXX is the identification number of thecluster of sequences to which the algorithm was applied, and YYYYY isthe number of the prediction generated by the algorithm, and N_(1,2,3) .. . , if present, represent specific exons that may have been manuallyedited during analysis (See Example V). Alternatively, thepolynucleotide fragments in column 2 may refer to assemblages of exonsbrought together by an “exon-stretching” algorithm. For example, apolynucleotide sequence identified as FLXXXXXX_gAAAAA_gBBBB_(—)1_N is a“stretched” sequence, with XXXX being the Incyte project identificationnumber, gAAAAA being the GenBank identification number of the humangenomnic sequence to which the “exon-stretching” algorithm was applied,gBBBBB being the GenBank identification number or NCBI RefSeqidentification number of the nearest GenBank protein homolog, and Nreferring to specific exons (See Example V). In instances where a RefSeqsequence was used as a protein homolog for the “exon-stretching”algorithm, a RefSeq identifier (denoted by “NM,” “NP,” or “NT”) may beused in place of the Genlank identifier (i.e., gBBBBB).

[0175] Alternatively, a prefix identifies component sequences that werehand-edited, predicted from genomic DNA sequences, or derived from acombination of sequence analysis methods. The following Table listsexamples of component sequence prefixes and corresponding sequenceanalysis methods associated with the prefixes (see Example IV andExample V). Prefix Type of analysis and/or examples of programs GNN,GFG, Exon prediction from genomic sequences using, ENST for example,GENSCAN (Stanford University, CA, USA) or FGENES (Computer GenomicsGroup, The Sanger Centre, Cambridge, UK). GBI Hand-edited analysis ofgenomic sequences. FL Stitched or stretched genomic sequences (seeExample V). INCY Full length transcript and exon prediction from mappingof EST sequences to the genome. Genomic location and EST compositiondata are combined to predict the exons and resulting transcript.

[0176] In some cases, Incyte cDNA coverage redundant with the sequencecoverage shown in Table 4 was obtained to confirm the final consensuspolynucleotide sequence, but the relevant Incyte cDNA identificationnumbers are not shown.

[0177] Table 5 shows the representative cDNA libraries for those fulllength polynucleotides which were assembled using Incyte cDNA sequences.The representative cDNA library is the Incyte cDNA library which is mostfrequently represented by the Incyte cDNA sequences which were used toassemble and confirm the above polynucleotides. The tissues and vectorswhich were used to construct the cDNA libraries shown in Table 5 aredescribed in Table 6.

[0178] Table 8 shows single nucleotide polymorphisms (SNPs) found inpolynucleotide sequences of the invention, along with allele frequenciesin different human populations. Columns 1 and 2 show the polynucleotidesequence identification number (SEQ ID NO:) and the corresponding Incyteproject identification number (PID) for polynucleotides of theinvention. Column 3 shows the Incyte identification number for the ESTin which the SNP was detected (EST ID), and column 4 shows theidentification number for the SNP(SNP ID). Column 5 shows the positionwithin the EST sequence at which the SNP is located (EST SNP), andcolumn 6 shows the position of the SNP within the full-lengthpolynucleotide sequence (CB1 SNP). Column 7 shows the allele found inthe EST sequence. Columns 8 and 9 show the two alleles found at the SNPsite. Column 10 shows the amino acid encoded by the codon including theSNP site, based upon the allele found in the EST. Columns 11-14 show thefrequency of allele 1 in four different human populations. An entry ofn/d (not detected) indicates that the frequency of allele 1 in thepopulation was too low to be detected, while n/a (not available)indicates that the allele frequency was not determined for thepopulation.

[0179] The invention also encompasses VAP variants. Various embodimentsof VAP variants can have at least about 80%, at least about 90%, or atleast about 95% amino acid sequence identity to the VAP amino acidsequence, and can contain at least one functional or structuralcharacteristic of VAP.

[0180] Various embodiments also encompass polynucleotides which encodeVAP. In a particular embodiment, the invention encompasses apolynucleotide sequence comprising a sequence selected from the groupconsisting of SEQ ID NO:21-40, which encodes VAP. The polynucleotidesequences of SEQ ID NO:21140, as presented in the Sequence Listing,embrace the equivalent RNA sequences, wherein occurrences of thenitrogenous base thymine are replaced with uracil, and the sugarbackbone is composed of ribose instead of deoxyribose.

[0181] The invention also encompasses variants of a polynucleotideencoding VAP. In particular, such a variant polynucleotide will have atleast about 70%, or alternatively at least about 85%, or even at leastabout 95% polynucleotide sequence identity to a polynucleotide encodingVAP. A particular aspect of the invention encompasses a variant of apolynucleotide comprising a sequence selected from the group consistingof SEQ ID NO:21-40 which has at least about 70%, or alternatively atleast about 85%, or even at least about 95% polynucleotide sequenceidentity to a nucleic acid sequence selected from the group consistingof SEQ ID NO:21-40. Any one of the polynucleotide variants describedabove can encode a polypeptide which contains at least one functional orstructural characteristic of VAP.

[0182] In addition, or in the alternative, a polynucleotide variant ofthe invention is a splice variant of a polynucleotide encoding VAP. Asplice variant may have portions which have significant sequenceidentity to a polynucleotide encoding VAP, but will generally have agreater or lesser number of polynucleotides due to additions ordeletions of blocks of sequence arising from alternate splicing of exonsduring mRNA processing. A splice variant may have less than about 70%,or alternatively less than about 60%, or alternatively less than about50% polynucleotide sequence identity to a polynucleotide encoding VAPover its entire length; however, portions of the splice variant willhave at least about 70%, or alternatively at least about 85%, oralternatively at least about 95%, or alternatively 100% polynucleotidesequence identity to portions of the polynucleotide encoding VAP. Forexample, a polynucleotide comprising a sequence of SEQ ID NO:30 and apolynucleotide comprising a sequence of SEQ ID NO:33 are splice variantsof each other. Any one of the splice variants described above can encodea polypeptide which contains at least one functional or structuralcharacteristic of VAP.

[0183] It will be appreciated by those skilled in the art that as aresult of the degeneracy of the genetic code, a multitude ofpolynucleotide sequences encoding VAP, some bearing minimal similarityto the polynucleotide sequences of any known and naturally occurringgene, may be produced. Thus, the invention contemplates each and everypossible variation of polynucleotide sequence that could be made byselecting combinations based on possible codon choices. Thesecombinations are made in accordance with the standard triplet geneticcode as applied to the polynucleotide sequence of naturally occurringVAP, and all such variations are to be considered as being specificallydisclosed.

[0184] Although polynucleotides which encode VAP and its variants aregenerally capable of hybridizing to polynucleotides encoding naturallyoccurring VAP under appropriately selected conditions of stringency, itmay be advantageous to produce polynucleotides encoding VAP or itsderivatives possessing a substantially different codon usage, e.g.,inclusion of non-naturally occurring codons. Codons may be selected toincrease the rate at which expression of the peptide occurs in aparticular prokaryotic or eukaryotic host in accordance with thefrequency with which particular codons are utilized by the host. Otherreasons for substantially altering the nucleotide sequence encoding VAPand its derivatives without altering the encoded amino acid sequencesinclude the production of RNA transcripts having more desirableproperties, such as a greater half-life, than transcripts produced fromthe naturally occurring sequence.

[0185] The invention also encompasses production of polynucleotideswhich encode VAP and VAP derivatives, or fragments thereof, entirely bysynthetic chemistry. After production, the synthetic polynucleotide maybe inserted into any of the many available expression vectors and cellsystems using reagents well known in the art. Moreover, syntheticchemistry may be used to introduce mutations into a polynucleotideencoding VAP or any fragment thereof.

[0186] Embodiments of the invention can also include polynucleotidesthat are capable of hybridizing to the claimed polynucleotides, and, inparticular, to those having the sequences shown in SEQ ID NO:21-40 andfragments thereof, under various conditions of stringency (Wahl, G. M.and S. L. Berger (1987) Methods Enzymol. 152:399407; Kimmel, A. R.(1987) Methods Enzymol. 152:507-511). Hybridization conditions,including annealing and wash conditions, are described in “Definitions.”

[0187] Methods for DNA sequencing are well known in the art and may beused to practice any of the embodiments of the invention. The methodsmay employ such enzymes as the Klenow fragment of DNA polymerase I,SEQUENASE (US Biochemical, Cleveland Ohio), Taq polymerase (AppliedBiosystems), thermostable T7 polymerase (Amersham Biosciences,Piscataway N.J.), or combinations of polymerases and proofreadingexonucleases such as those found in the ELONGASE amplification system(Invitrogen, Carlsbad Calif.). Preferably, sequence preparation isautomated with machines such as the MICROLAB 2200 liquid transfer system(Hamilton, Reno Nev.), PTC200 thermal cycler (MJ Research, WatertownMass.) and ABI CATALYST 800 thermal cycler (Applied Biosystems).Sequencing is then carried out using either the ABI 373 or 377 DNAsequencing system (Applied Biosystems), the MEGABACE 1000 DNA sequencingsystem (Amersham Biosciences), or other systems known in the art. Theresulting sequences are analyzed using a variety of algorithms which arewell known in the art (Ausubel et al., supra, ch. 7; Meyers, R. A.(1995) Molecular Biology and Biotechnology, Wiley VCH, New York N.Y.,pp. 856-853).

[0188] The nucleic acids encoding VAP may be extended utilizing apartial nucleotide sequence and employing various PCR-based methodsknown in the art to detect upstream sequences, such as promoters andregulatory elements. For example, one method which may be employed,restriction-site PCR, uses universal and nested primers to amplifyunknown sequence from genomic DNA within a cloning vector (Sarkar, G.(1993) PCR Methods Applic. 2:318-322). Another method, inverse PCR, usesprimers that extend in divergent directions to amplify unknown sequencefrom a circularized template. The template is derived from restrictionfragments comprising a known genomic locus and surrounding sequences(Triglia, T. et al. (1988) Nucleic Acids Res. 16:8186). A third method,capture PCR, involves PCR amplification of DNA fragments adjacent toknown sequences in human and yeast artificial chromosome DNA(Lagerstrom, M. et al. (1991) PCR Methods Applic. 1: 111-119). In thismethod, multiple restriction enzyme digestions and ligations may be usedto insert an engineered double-stranded sequence into a region ofunknown sequence before performing PCR. Other methods which may be usedto retrieve unknown sequences are known in the art (Parker, J. D. et al.(1991) Nucleic Acids Res. 19:3055-3060). Additionally, one may use PCR,nested primers, and PROMOTERFINDER libraries (Clontech, Palo AltoCalif.) to walk genomic DNA. This procedure avoids the need to screenlibraries and is useful in finding intron/exon junctions. For allPCR-based methods, primers may be designed using commercially availablesoftware, such as OLIGO 4.06 primer analysis software (NationalBiosciences, Plymouth Minn.) or another appropriate program, to be about22 to 30 nucleotides in length, to have a GC content of about 50% ormore, and to anneal to the template at temperatures of about 68° C. to72° C.

[0189] When screening for full length cDNAs, it is preferable to uselibraries that have been size-selected to include larger cDNAs. Inaddition, random-primed libraries, which often include sequencescontaining the 5′ regions of genes, are preferable for situations inwhich an oligo d(T) library does not yield a full-length cDNA. Genomiclibraries may be useful for extension of sequence into 5′non-transcribed regulatory regions.

[0190] Capillary electrophoresis systems which are commerciallyavailable may be used to analyze the size or confirm the nucleotidesequence of sequencing or PCR products. In particular, capillarysequencing may employ flowable polymers for electrophoretic separation,four different nucleotide-specific, laser-stimulated fluorescent dyes,and a charge coupled device camera for detection of the emittedwavelengths. Output/light intensity may be converted to electricalsignal using appropriate software (e.g., GENOTYPER and SEQUENCENAVIGATOR, Applied Biosystems), and the entire process from loading ofsamples to computer analysis and electronic data display may be computercontrolled. Capillary electrophoresis is especially preferable forsequencing small DNA fragments which may be present in limited amountsin a particular sample.

[0191] In another embodiment of the invention, polynucleotides orfragments thereof which encode VAP may be cloned in recombinant DNAmolecules that direct expression of VAP, or fragments or functionalequivalents thereof, in appropriate host cells. Due to the inherentdegeneracy of the genetic code, other polynucleotides which encodesubstantially the same or a functionally equivalent polypeptides may beproduced and used to express VAP.

[0192] The polynucleotides of the invention can be engineered usingmethods generally known in the art in order to alter VAP-encodingsequences for a variety of purposes including, but not limited to,modification of the cloning, processing, and/or expression of the geneproduct. DNA shuffling by random fragmentation and PCR reassembly ofgene fragments and synthetic oligonucleotides may be used to engineerthe nucleotide sequences. For example, oligonucleotide-mediatedsite-directed mutagenesis may be used to introduce mutations that createnew restriction sites, alter glycosylation patterns, change codonpreference, produce splice variants, and so forth.

[0193] The nucleotides of the present invention may be subjected to DNAshuffling techniques such as MOLECULARBREEDING (Maxygen Inc., SantaClara Calif.; described in U.S. Pat. No. 5,837,458; Chang, C.-C. et al.(1999) Nat. Biotechnol. 17:793-797; Christians, F. C. et al. (1999) Nat.Biotechnol. 17:259-264; and Crameri, A. et al. (1996) Nat. Biotechnol.14:315-319) to alter or improve the biological properties of VAP, suchas its biological or enzymatic activity or its ability to bind to othermolecules or compounds. DNA shuffling is a process by which a library ofgene variants is produced using PCR-mediated recombination of genefragments. The library is then subjected to selection or screeningprocedures that identify those gene variants with the desiredproperties. These preferred variants may then be pooled and furthersubjected to recursive rounds of DNA shuffling and selection/screening.Thus, genetic diversity is created through “artificial” breeding andrapid molecular evolution. For example, fragments of a single genecontaining random point mutations may be recombined, screened, and thenreshuffled until the desired properties are optimized. Alternatively,fragments of a given gene may be recombined with fragments of homologousgenes in the same gene family, either from the same or differentspecies, thereby maximizing the genetic diversity of multiple naturallyoccurring genes in a directed and controllable manner.

[0194] In another embodiment, polynucleotides encoding VAP may besynthesized, in whole or in part, using one or more chemical methodswell known in the art (Caruthers, M. H. et al. (1980) Nucleic AcidsSymp. Ser. 7:215-223; Horn, T. et al. (1980) Nucleic Acids Symp. Ser.7:225-232). Alternatively, VAP itself or a fragment thereof may besynthesized using chemical methods known in the art. For example,peptide synthesis can be performed using various solution-phase orsolid-phase techniques (Creighton, T. (1984) Proteins, Structures andMolecular Properties, WH Freeman, New York N.Y., pp. 55-60; Roberge, J.Y. et al. (1995) Science 269:202-204). Automated synthesis may beachieved using the ABI 431A peptide synthesizer (Applied Biosystems).Additionally, the amino acid sequence of VAP, or any part thereof, maybe altered during direct synthesis and/or combined with sequences fromother proteins, or any part thereof, to produce a variant polypeptide ora polypeptide having a sequence of a naturally occurring polypeptide.

[0195] The peptide may be substantially purified by preparative highperformance liquid chromatography (Chiez, R. M. and F. Z. Regnier (1990)Methods Enzymol. 182:392421). The composition of the synthetic peptidesmay be confirmed by amino acid analysis or by sequencing (Creighton,supra, pp. 28-53).

[0196] In order to express a biologically active VAP, thepolynucleotides encoding VAP or derivatives thereof may be inserted intoan appropriate expression vector, i.e., a vector which contains thenecessary elements for transcriptional and translational control of theinserted coding sequence in a suitable host. These elements includeregulatory sequences, such as enhancers, constitutive and induciblepromoters, and 5′ and 3′ untranslated regions in the vector and inpolynucleotides encoding VAP. Such elements may vary in their strengthand specificity. Specific initiation signals may also be used to achievemore efficient translation of polynucleotides encoding VAP. Such signalsinclude the ATG initiation codon and adjacent sequences, e.g. the Kozaksequence. In cases where a polynucleotide sequence encoding VAP and itsinitiation codon and upstream regulatory sequences are inserted into theappropriate expression vector, no additional transcriptional ortranslational control signals may be needed. However, in cases whereonly coding sequence, or a fragment thereof, is inserted, exogenoustranslational control signals including an in-frame ATG initiation codonshould be provided by the vector. Exogenous translational elements andinitiation codons may be of various origins, both natural and synthetic.The efficiency of expression may be enhanced by the inclusion ofenhancers appropriate for the particular host cell system used (Scharf,D. et al. (1994) Results Probl. Cell Differ. 20:125-162).

[0197] Methods which are well known to those skilled in the art may beused to construct expression vectors containing polynucleotides encodingVAP and appropriate transcriptional and translational control elements.These methods include in vitro recombinant DNA techniques, synthetictechniques, and in vivo genetic recombination (Sambrook and Russell,supra, ch. 1-4, and 8; Ausubel et al., supra, ch. 1, 3, and 15).

[0198] A variety of expression vector/host systems may be utilized tocontain and express polynucleotides encoding VAP. These include, but arenot limited to, microorganisms such as bacteria transformed withrecombinant bacteriophage, plasmid, or cosmid DNA expression vectors;yeast transformed with yeast expression vectors; insect cell systemsinfected with viral expression vectors (e.g., baculovirus); plant cellsystems transformed with viral expression vectors (e.g., cauliflowermosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterialexpression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems(Sambrook and Russell, supra; Ausubel et al., supra; Van Heeke, G. andS. M. Schuster (1989) J. Biol. Chem. 264:5503-5509; Engelhard, E. K. etal. (1994) Proc. Natl. Acad. Sci. USA 91:3224-3227; Sandig, V. et al.(1996) Hum. Gene Ther. 7:1937-1945; Takamatsu, N. (1987) EMBO J.6:307-311; The McGraw Hill Yearbook of Science and Technology (1992)McGraw Hill, New York N.Y., pp. 191-196; Logan, J. and T. Shenk (1984)Proc. Natl. Acad. Sci. USA 81:3655-3659; Harrington, J. J. et al. (1997)Nat. Genet. 15:345-355). Expression vectors derived from retroviruses,adenoviruses, or herpes or vaccinia viruses, or from various bacterialplasmids, may be used for delivery of polynucleotides to the targetedorgan, tissue, or cell population (Di Nicola, M. et al. (1998) CancerGen. Ther. 5:350-356; Yu, M. et al. (1993) Proc. Natl. Acad. Sci. USA90:6340-6344; Buller, R. M. et al. (1985) Nature 317:813-815; McGregor,D. P. et al. (1994) Mol. Immunol. 31:219-226; Verma, I. M. and N. Somia(1997) Nature 389:239-242). The invention is not limited by the hostcell employed.

[0199] In bacterial systems, a number of cloning and expression vectorsmay be selected depending upon the use intended for polynucleotidesencoding VAP. For example, routine cloning, subcloning, and propagationof polynucleotides encoding VAP can be achieved using a multifunctionalE. coli vector such as PBLUESCRIPT (Stratagene, La Jolla Calif.) orPSPORT1 plasmid (Invitrogen). Ligation of polynucleotides encoding VAPinto the vector's multiple cloning site disrupts the lacZ gene, allowinga calorimetric screening procedure for identification of transformedbacteria containing recombinant molecules. In addition, these vectorsmay be useful for in vitro transcription, dideoxy sequencing, singlestrand rescue with helper phage, and creation of nested deletions in thecloned sequence (Van Heeke, G. and S. M. Schuster (1989) J. Biol. Chem.264:5503-5509). When large quantities of VAP are needed, e.g. for theproduction of antibodies, vectors which direct high level expression ofVAP may be used. For example, vectors containing the strong, inducibleSP6 or 17 bacteriophage promoter may be used.

[0200] Yeast expression systems may be used for production of VAP. Anumber of vectors containing constitutive or inducible promoters, suchas alpha factor, alcohol oxidase, and PGH promoters, may be used in theyeast Saccharomyces cerevisiae or Pichia pastoris. In addition, suchvectors direct either the secretion or intracellular retention ofexpressed proteins and enable integration of foreign polynucleotidesequences into the host genome for stable propagation (Ausubel et al.,supra; Bitter, G. A. et al. (1987) Methods Enzymol. 153:516-544; Scorer,C. A. et al. (1994) Bio/Technology 12:181-184).

[0201] Plant systems may also be used for expression of VAP.Transcription of polynucleotides encoding VAP may be driven by viralpromoters, e.g., the ³⁵S and 19S promoters of CaMV used alone or incombination with the omega leader sequence from TMV (Takamatsu, N.(1987) EMBO J. 6:307-311). Alternatively, plant promoters such as thesmall subunit of RUBISCO or heat shock promoters may be used (Coruzzi,G. et al. (1984) EMBO J. 3:1671-1680; Broglie, R. et al. (1984) Science224:838-843; Winter, J. et al. (1991) Results Probl. Cell Differ.17:85-105). These constructs can be introduced into plant cells bydirect DNA transformation or pathogen-mediated transfection (The McGrawHill Yearbook of Science and Technology (1992) McGraw Hill, New YorkN.Y., pp. 191-196).

[0202] In mammalian cells, a number of viral-based expression systemsmay be utilized. In cases where an adenovirus is used as an expressionvector, polynucleotides encoding VAP may be ligated into an adenovirustranscription/translation complex consisting of the late promoter andtripartite leader sequence. Insertion in a non-essential E1 or E3 regionof the viral genome may be used to obtain infective virus whichexpresses VAP in host cells (Logan, J. and T. Shenk (1984) Proc. Natl.Acad. Sci. USA 81:3655-3659). In addition, transcription enhancers, suchas the Rous sarcoma virus (RSV) enhancer, may be used to increaseexpression in mammalian host cells. SV40 or EBV-based vectors may alsobe used for high-level protein expression.

[0203] Human artificial chromosomes (HACs) may also be employed todeliver larger fragments of DNA than can be contained in and expressedfrom a plasmid. HACs of about 6 kb to 10 Mb are constructed anddelivered via conventional delivery methods (liposomes, polycationicamino polymers, or vesicles) for therapeutic purposes (Harrington, J. J.et al. (1997) Nat. Genet. 15:345-355).

[0204] For long term production of recombinant proteins in manmmaliansystems, stable expression of VAP in cell lines is preferred. Forexample, polynucleotides encoding VAP can be transformed into cell linesusing expression vectors which may contain viral origins of replicationand/or endogenous expression elements and a selectable marker gene onthe same or on a separate vector. Following the introduction of thevector, cells may be allowed to grow for about 1 to 2 days in enrichedmedia before being switched to selective media. The purpose of theselectable marker is to confer resistance to a selective agent, and itspresence allows growth and recovery of cells which successfully expressthe introduced sequences. Resistant clones of stably transformed cellsmay be propagated using tissue culture techniques appropriate to thecell type.

[0205] Any number of selection systems may be used to recovertransformed cell lines. These include, but are not limited to, theherpes simplex virus thymidine kinase and adeninephosphoribosyltransferase genes, for use in tk⁻ and apr^(·) cells,respectively (Wigler, M. et al. (1977) Cell 11:223-232; Lowy, I. et al.(1980) Cell 22:817-823). Also, antimetabolite, antibiotic, or herbicideresistance can be used as the basis for selection. For example, dlfrconfers resistance to methotrexate; neo confers resistance to theaminoglycosides neomycin and GA418; and als and pat confer resistance tochlorsulfuron and phosphinotricin acetyltransferase, respectively(Wigler, M. et al. (1980) Proc. Natl. Acad. Sci. USA 77:3567-3570;Colbere-Garapin, F. et al. (1981) J. Mol. Biol. 150:1-14). Additionalselectable genes have been described, e.g., trpB and hisD, which altercellular requirements for metabolites (Hartman, S. C. and R. C. Mulligan(1988) Proc. Natl. Acad. Sci. USA 85:8047-8051). Visible markers, e.g.,anthocyanins, green fluorescent proteins (GFP; Clontech),β-glucuronidase and its substrate β-glucuronide, or luciferase and itssubstrate luciferin may be used. These markers can be used not only toidentify transformants, but also to quantify the amount of transient orstable protein expression attributable to a specific vector system(Rhodes, C. A. (1995) Methods Mol. Biol. 55:121-131).

[0206] Although the presence/absence of marker gene expression suggeststhat the gene of interest is also present, the presence and expressionof the gene may need to be confirmed. For example, if the sequenceencoding VAP is inserted within a marker gene sequence, transformedcells containing polynucleotides encoding VAP can be identified by theabsence of marker gene function. Alternatively, a marker gene can beplaced in tandem with a sequence encoding VAP under the control of asingle promoter. Expression of the marker gene in response to inductionor selection usually indicates expression of the tandem gene as well.

[0207] In general, host cells that contain the polynucleotide encodingVAP and that express VAP may be identified by a variety of proceduresknown to those of skill in the art. These procedures include, but arenot limited to, DNA-DNA or DNA-RNA hybridizations, PCR amplification,and protein bioassay or immunoassay techniques which include membrane,solution, or chip based technologies for the detection and/orquantification of nucleic acid or protein sequences.

[0208] Immunological methods for detecting and measuring the expressionof VAP using either specific polyclonal or monoclonal antibodies areknown in the art. Examples of such techniques include enzymeinkedimmunosorbent assays (ELISAs), radioimmunoassays (RIAs), andfluorescence activated cell sorting (FACS). A two-site, monoclonal-basedimmunoassay utilizing monoclonal antibodies reactive to twonon-interfering epitopes on VAP is preferred, but a competitive bindingassay may be employed. These and other assays are well known in the art(Hampton, R. et al. (1990) Serological Methods, a Laboratory Manual, APSPress, St. Paul Minn., Sect. IV; Coligan, J. E. et al. (1997) CurrentProtocols in Immunology, Greene Pub. Associates and Wiley-Interscience,New York N.Y.; Pound, J. D. (1998) Immunochemical Protocols, HumanaPress, Totowa N.J.).

[0209] A wide variety of labels and conjugation techniques are known bythose skilled in the art and may be used in various nucleic acid andamino acid assays. Means for producing labeled hybridization or PCRprobes for detecting sequences related to polynucleotides encoding VAPinclude oligolabeling, nick translation, end-labeling, or PCRamplification using a labeled nucleotide. Alternatively, polynucleotidesencoding VAP, or any fragments thereof, may be cloned into a vector forthe production of an mRNA probe. Such vectors are known in the art, arecommercially available, and may be used to synthesize RNA probes invitro by addition of an appropriate RNA polymerase such as T7, T3, orSP6 and labeled nucleotides. These procedures may be conducted using avariety of commercially available kits, such as those provided byAmersham Biosciences, Promega (Madison W), and US Biochemical. Suitablereporter molecules or labels which may be used for ease of detectioninclude radionuclides, enzymes, fluorescent, cherniluminescent, orchromogenic agents, as well as substrates, cofactors, inhibitors,magnetic particles, and the like.

[0210] Host cells transformed with polynucleotides encoding VAP may becultured under conditions suitable for the expression and recovery ofthe protein from cell culture. The protein produced by a transformedcell may be secreted or retained intracellularly depending on thesequence and/or the vector used. As will be understood by those of skillin the art, expression vectors containing polynucleotides which encodeVAP may be designed to contain signal sequences which direct secretionof VAP through a prokaryotic or eukaryotic cell membrane.

[0211] In addition, a host cell strain may be chosen for its ability tomodulate expression of the inserted polynucleotides or to process theexpressed protein in the desired fashion. Such modifications of thepolypeptide include, but are not limited to, acetylation, carboxylation,glycosylation, phosphorylation, lipidation, and acylation.Post-translational processing which cleaves a “prepro” or “pro” form ofthe protein may also be used to specify protein targeting, folding,and/or activity. Different host cells which have specific cellularmachinery and characteristic mechanisms for post-translationalactivities (e.g., CHO, HeLa, MDCK, HBEK293, and W138) are available fromthe American Type Culture Collection (ATCC, Manassas Va.) and may bechosen to ensure the correct modification and processing of the foreignprotein.

[0212] In another embodiment of the invention, natural, modified, orrecombinant polynucleotides encoding VAP may be ligated to aheterologous sequence resulting in translation of a fusion protein inany of the aforementioned host systems. For example, a chimeric VAPprotein containing a heterologous moiety that can be recognized by acommercially available antibody may facilitate the screening of peptidelibraries for inhibitors of VAP activity. Heterologous protein andpeptide moieties may also facilitate purification of fusion proteinsusing commercially available affinity matrices. Such moieties include,but are not limited to, glutathione S-transferase (GST), maltose bindingprotein (MBP), thioredoxin (Trx), calmodulin binding peptide (CBP),6-His, FLAG, c-nzyc, and hemagglutinin (HA). GST, MBP, Trx, CBP, and6-His enable purification of their cognate fusion proteins onimmobilized glutathione, maltose, phenylarsine oxide, calmodulin, andmetal-chelate resins, respectively. FLAG, c-myc, and hemagglutinin (HA)enable immunoaffinity purification of fusion proteins using commerciallyavailable monoclonal and polyclonal antibodies that specificallyrecognize these epitope tags. A fusion protein may also be engineered tocontain a proteolytic cleavage site located between the VAP encodingsequence and the heterologous protein sequence, so that VAP may becleaved away from the heterologous moiety following purification.Methods for fusion protein expression and purification are discussed inAusubel et al. (supra, ch. 10 and 16). A variety of commerciallyavailable kits may also be used to facilitate expression andpurification of fusion proteins.

[0213] In another embodiment, synthesis of radiolabeled VAP may beachieved in vitro using the TNT rabbit reticulocyte lysate or wheat germextract system (Promega). These systems couple transcription andtranslation of protein-coding sequences operably associated with the T7,T3, or SP6 promoters. Translation takes place in the presence of aradiolabeled amino acid precursor, for example, ³⁵S-methionine.

[0214] VAP, fragments of VAP, or variants of VAP may be used to screenfor compounds that specifically bind to VAP. One or more test compoundsmay be screened for specific binding to VAP. In various embodiments, 1,2, 3, 4, 5, 10, 20, 50, 100, or 200 test compounds can be screened forspecific binding to VAP. Examples of test compounds can includeantibodies, anticalins, oligonucleotides, proteins (e.g., ligands orreceptors), or small molecules.

[0215] In related embodiments, variants of VAP can be used to screen forbinding of test compounds, such as antibodies, to VAP, a variant of VAP,or a combination of VAP and/or one or more variants VAP. In anembodiment, a variant of VAP can be used to screen for compounds thatbind to a variant of VAP, but not to VAP having the exact sequence of asequence of SEQ ID NO:1-20. VAP variants used to perform such screeningcan have a range of about 50% to about 99% sequence identity to VAP,with various embodiments having 60%, 70%, 75%, 80%, 85%, 90%, and 95%sequence identity.

[0216] In an embodiment, a compound identified in a screen for specificbinding to VAP can be closely related to the natural ligand of VAP,e.g., a ligand or fragment thereof, a natural substrate, a structural orfunctional mimetic, or a natural binding partner (Coligan, J. E. et al.(1991) Current Protocols in Immunology 1(2):Chapter 5). In anotherembodiment, the compound thus identified can be a natural ligand of areceptor VAP (Howard, A. D. et al. (2001) Trends Pharmacol. Sci. 22:132-140; Wise, A. et al. (2002) Drug Discovery Today 7:235-246).

[0217] In other embodiments, a compound identified in a screen forspecific binding to VAP can be losely related to the natural receptor towhich VAP binds, at least a fragment of the receptor, or a ragment ofthe receptor including all or a portion of the ligand binding site orbinding pocket. For example, the compound may be a receptor for VAPwhich is capable of propagating a signal, or a decoy receptor for VAPwhich is not capable of propagating a signal (Ashkenazi, A. and V. M.Divit (1999) Curr. Opin. Cell Biol. 11:255-260; Mantovani, A. et al.(2001) Trends Immunol. 22:328-336).

[0218] The compound can be rationally designed using known techniques.Examples of such techniques include those used to construct the compoundetanercept (ENBREL; Amgen Inc., Thousand Oaks Calif.), which isefficacious for treating rheumatoid arthritis in humans. Etanercept isan engineered p75 tumor necrosis factor (TNF) receptor dimer linked tothe Fc portion of human IgG1 (Taylor, P. C. et al. (2001) Curr. Opin.Immunol. 13:611-616).

[0219] In one embodiment, two or more antibodies having similar or,alternatively, different specificities can be screened for specificbinding to VAP, fragments of VAP, or variants of VAP. The bindingspecificity of the antibodies thus screened can thereby be selected toidentify particular fragments or variants of VAP. In one embodiment, anantibody can be selected such that its binding specificity allows forpreferential identification of specific fragments or variants of VAP. Inanother embodiment, an antibody can be selected such that its bindingspecificity allows for preferential diagnosis of a specific disease orcondition having increased, decreased, or otherwise abnormal productionof VAP.

[0220] In an embodiment, anticalins can be screened for specific bindingto VAP, fragments of VAP, or variants of VAP. Anticalins areligand-binding proteins that have been constructed based on a lipocalinscaffold (Weiss, G. A. and H. B. Lowman (2000) Chem. Biol. 7:R177-R184;Skerra, A. (2001) J. Biotechnol. 74:257-275). The protein architectureof lipocalins can include a beta-barrel having eight antiparallelbeta-strands, which supports four loops at its open end. These loopsform the natural ligand-binding site of the lipocalins, a site which canbe re-engineered in vitro by amino acid substitutions to impart novelbinding specificities. The amino acid substitutions can be made usingmethods known in the art or described herein, and can includeconservative substitutions (e.g., substitutions that do not alterbinding specificity) or substitutions that modestly, moderately, orsignificantly alter binding specificity.

[0221] In one embodiment, screening for compounds which specificallybind to, stimulate, or inhibit VAP involves producing appropriate cellswhich express VAP, either as a secreted protein or on the cell membrane.Preferred cells can include cells from mammals, yeast, Drosophila, or E.coli. Cells expressing VAP or cell membrane fractions which contain VAPare then contacted with a test compound and binding, stimulation, orinhibition of activity of either VAP or the compound is analyzed.

[0222] An assay may simply test binding of a test compound to thepolypeptide, wherein binding is detected by a fluorophore, radioisotope,enzyme conjugate, or other detectable label. For example, the assay maycomprise the steps of combining at least one test compound with VAP,either in solution or affixed to a solid support, and detecting thebinding of VAP to the compound. Alternatively, the assay may detect ormeasure binding of a test compound in the presence of a labeledcompetitor. Additionally, the assay may be carried out using cell-freepreparations, chemical libraries, or natural product mixtures, and thetest compound(s) may be free in solution or affixed to a solid support.

[0223] An assay can be used to assess the ability of a compound to bindto its natural ligand and/or to inhibit the binding of its naturalligand to its natural receptors. Examples of such assays includeradio-labeling assays such as those described in U.S. Pat. No. 5,914,236and U.S. Pat. No. 6,372,724. In a related embodiment, one or more aminoacid substitutions can be introduced into a polypeptide compound (suchas a receptor) to improve or alter its ability to bind to its naturalligands (Matthews, D. J. and J. A. Wells. (1994) Chem. Biol. 1:25-30).In another related embodiment, one or more amino acid substitutions canbe introduced into a polypeptide compound (such as a ligand) to improveor alter its ability to bind to its natural receptors (Cunningham, B. C.and J. A. Wells (1991) Proc. Natl. Acad. Sci. USA 88:3407-3411; Lowman,H. B. et al. (1991) J. Biol. Chem. 266:10982-10988).

[0224] VAP, fragments of VAP, or variants of VAP may be used to screenfor compounds that modulate the activity of VAP. Such compounds mayinclude agonists, antagonists, or partial or inverse agonists. In oneembodiment, an assay is performed under conditions permissive for VAPactivity, wherein VAP is combined with at least one test compound, andthe activity of VAP in the presence of a test compound is compared withthe activity of VAP in the absence of the test compound. A change in theactivity of VAP in the presence of the test compound is indicative of acompound that modulates the activity of VAP. Alternatively, a testcompound is combined with an in vitro or cell-free system comprising VAPunder conditions suitable for VAP activity, and the assay is performed.In either of these assays, a test compound which modulates the activityof VAP may do so indirectly and need not come in direct contact with thetest compound. At least one and up to a plurality of test compounds maybe screened.

[0225] In another embodiment, polynucleotides encoding VAP or theirmammalian homologs may be “knocked out” in an animal model system usinghomologous recombination in embryonic stem (ES) cells. Such techniquesare well known in the art and are useful for the generation of animalmodels of human disease (see, e.g., U.S. Pat. No. 5,175,383 and U.S.Pat. No. 5,767,337). For example, mouse ES cells, such as the mouse129/SvJ cell line, are derived from the early mouse embryo and grown inculture. The ES cells are transformed with a vector containing the geneof interest disrupted by a marker gene, e.g., the neomycinphosphotransferase gene (neo; Capecchi, M. R. (1989) Science244:1288-1292). The vector integrates into the corresponding region ofthe host genome by homologous recombination. Alternatively, homologousrecombination takes place using the Cre-loxP system to knockout a geneof interest in a tissue- or developmental stage-specific manner (Marth,J. D. (1996) Clin. Invest. 97:1999-2002; Wagner, K. U. et al. (1997)Nucleic Acids Res. 25:4323-4330). Transformed ES cells are identifiedand microinjected into mouse cell blastocysts such as those from theC57BL/6 mouse strain. The blastocysts are surgically transferred topseudopregnant dams, and the resulting chimeric progeny are genotypedand bred to produce heterozygous or homozygous strains. Transgenicanimals thus generated may be tested with potential therapeutic or toxicagents.

[0226] Polynucleotides encoding VAP may also be manipulated in vitro inES cells derived from human blastocysts. Human ES cells have thepotential to differentiate into at least eight separate cell lineagesincluding endoderm, mesoderm, and ectodermal cell types. These celllineages differentiate into, for example, neural cells, hematopoieticlineages, and cardiomyocytes (Thomson, J. A. et al. (1998) Science282:1145-1147).

[0227] Polynucleotides encoding VAP can also be used to create “knockin”humanized animals (pigs) or transgenic animals (mice or rats) to modelhuman disease. With knockin technology, a region of a polynucleotideencoding VAP is injected into animal ES cells, and the injected sequenceintegrates into the animal cell genome. Transformed cells are injectedinto blastulae, and the blastulae are implanted as described above.Transgenic progeny or inbred lines are studied and treated withpotential pharmaceutical agents to obtain information on treatment of ahuman disease. Alternatively, a mammal inbred to overexpress VAP, e.g.,by secreting VAP in its milk, may also serve as a convenient source ofthat protein (Janne, J. et al. (1998) Biotechnol. Annu. Rev. 4:55-74).

[0228] Therapeutics

[0229] Chemical and structural similarity, e.g., in the context ofsequences and motifs, exists between regions of VAP andvesicle-associated proteins. Expression of VAP is closely associatedwith lung tissue, ovary tissue, prostatic tumor tissue, adipocytetissue, metastatic bone marrow neuroblastoma tissue, brain tissue, colontissue, testiular tissue, and muscle tissue. In addition, examples oftissues expressing VAP can be found in Table 6 and can also be found inExample XI. Therefore, VAP appears to play a role in vesicle traffickingdisorders, autoimmune/inflammatory disorders, and cancer. In thetreatment of disorders associated with increased VAP expression oractivity, it is desirable to decrease the expression or activity of VAP.In the treatment of disorders associated with decreased VAP expressionor activity, it is desirable to increase the expression or activity ofVAP.

[0230] Therefore, in one embodiment, VAP or a fragment or derivativethereof may be administered to a subject to treat or prevent a disorderassociated with decreased expression or activity of VAP. Examples ofsuch disorders include, but are not limited to, a vesicle traffickingdisorder, such as cystic fibrosis, glucose-galactose malabsorptionsyndrome, hypercholesterolemia, diabetes mellitus, diabetes insipidus,hyper- and hypoglycemia, Grave's disease, goiter, Cushing's disease, andAddison's disease, gastrointestinal disorders including ulcerativecolitis, gastric and duodenal ulcers, other conditions associated withabnormal vesicle trafficking, including acquired immunodeficiencysyndrome (AIDS), allergies including hay fever, asthma, and urticaria(hives), autoimmune hemolytic anemia, proliferative glomerulonephritis,inflammatory bowel disease, multiple sclerosis, myasthenia gravis,rheumatoid and osteoarthritis, scleroderma, Chediak-Higashi andSjogren's syndromes, systemic lupus erythematosus, toxic shock syndrome,traumatic tissue damage, and viral, bacterial, fungal, helminthic, andprotozoal infections; an autoimmune/inflammatory disorder, such asacquired immunodeficiency syndrome (AIDS), Addison's disease, adultrespiratory distress syndrome, allergies, ankylosing spondylitis,amyloidosis, anemia, asthma, atherosclerosis, autoimmune hemolyticanemia, autoimmune thyroiditis, autoimmunepolyendocrinopathy-candidiasis-ectodermal dystrophy (APECED),bronchitis, cholecystitis, contact dermatitis, Crohn's disease, atopicdermatitis, dermatomyositis, diabetes mellitus, emphysema, episodiclymphopenia with lymphocytotoxins, erythroblastosis fetalis, erythemanodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome,gout, Graves' disease, Hashimoto's thyroiditis, hypereosinophilia,irritable bowel syndrome, multiple sclerosis, myasthenia gravis,myocardial or pericardial inflammation, osteoarthritis, osteoporosis,pancreatitis, polymyositis, psoriasis, Reiter's syndrome, rheumatoidarthritis, scleroderma, Sjogren's syndrome, systemic anaphylaxis,systemic lupus erythematosus, systemic sclerosis, thrombocytopenicpurpura, ulcerative colitis, uveitis, Werner syndrome, complications ofcancer, hemodialysis, and extracorporeal circulation, viral, bacterial,fungal, parasitic, protozoal, and helminthic infections, and trauma; anda cancer, such as adenocarcinoma, leukemia, lymphoma, melanoma, myeloma,sarcoma, teratocarcinoma, and, in particular, cancers of the adrenalgland, bladder, bone, bone marrow, brain, breast, cervix, colon, gallbladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung,muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands,skin, spleen, testis, thymus, thyroid, and uterus.

[0231] In another embodiment, a vector capable of expressing VAP or afragment or derivative thereof may be administered to a subject to treator prevent a disorder associated with decreased expression or activityof VAP including, but not limited to, those described above.

[0232] In a further embodiment, a composition comprising a substantiallypurified VAP in conjunction with a suitable pharmaceutical carrier maybe administered to a subject to treat or prevent a disorder associatedwith decreased expression or activity of VAP including, but not limitedto, those provided above.

[0233] In still another embodiment, an agonist which modulates theactivity of VAP may be administered to a subject to treat or prevent adisorder associated with decreased expression or activity of VAPincluding, but not limited to, those listed above.

[0234] In a further embodiment, an antagonist of VAP may be administeredto a subject to treat or prevent a disorder associated with increasedexpression or activity of VAP. Examples of such disorders include, butare not limited to, those vesicle trafficking disorders,autoimmune/inflammatory disorders, and cancer described above. In oneaspect, an antibody which specifically binds VAP may be used directly asan antagonist or indirectly as a targeting or delivery mechanism forbringing a pharmaceutical agent to cells or tissues which express VAP.

[0235] In an additional embodiment, a vector expressing the complementof the polynucleotide encoding VAP may be administered to a subject totreat or prevent a disorder associated with increased expression oractivity of VAP including, but not limited to, those described above.

[0236] In other embodiments, any protein, agonist, antagonist, antibody,complementary sequence, or vector embodiments may be administered incombination with other appropriate therapeutic agents. Selection of theappropriate agents for use in combination therapy may be made by one ofordinary skill in the art, according to conventional pharmaceuticalprinciples. The combination of therapeutic agents may actsynergistically to effect the treatment or prevention of the variousdisorders described above. Using this approach, one may be able toachieve therapeutic efficacy with lower dosages of each agent, thusreducing the potential for adverse side effects.

[0237] An antagonist of VAP may be produced using methods which aregenerally known in the art. In particular, purified VAP may be used toproduce antibodies or to screen libraries of pharmaceutical agents toidentify those which specifically bind VAP. Antibodies to VAP may alsobe generated using methods that are well known in the art. Suchantibodies may include, but are not limited to, polyclonal, monoclonal,chimeric, and single chain antibodies, Fab fragments, and fragmentsproduced by a Fab expression library. In an embodiment, neutralizingantibodies (i.e., those which inhibit dimer formation) can be usedtherapeutically. Single chain antibodies (e.g., from camels or llamas)may be potent enzyme inhibitors and may have application in the designof peptide mimetics, and in the development of immuno-adsorbents andbiosensors (Muyldermans, S. (2001) J. Biotechnol. 74:277-302).

[0238] For the production of antibodies, various hosts including goats,rabbits, rats, mice, camels, dromedaries, llamas, humans, and others maybe immunized by injection with VAP or with any fragment or oligopeptidethereof which has immunogenic properties. Depending on the host species,various adjuvants may be used to increase immunological response. Suchadjuvants include, but are not limited to, Freund's, mineral gels suchas aluminum hydroxide, and surface active substances such aslysolecithin, pluronic polyols, polyanions, peptides, oil emulsions,KLH, and dinitrophenol. Among adjuvants used in humans, BCG (bacilliCalmette-Guerin) and Corynebacterium parvum are especially preferable.

[0239] It is preferred that the oligopeptides, peptides, or fragmentsused to induce antibodies to VAP have an amino acid sequence consistingof at least about 5 amino acids, and generally will consist of at leastabout 10 amino acids. It is also preferable that these oligopeptides,peptides, or fragments are substantially identical to a portion of theamino acid sequence of the natural protein. Short stretches of VAP aminoacids may be fused with those of another protein, such as KLH, andantibodies to the chimeric molecule may be produced.

[0240] Monoclonal antibodies to VAP may be prepared using any techniquewhich provides for the production of antibody molecules by continuouscell lines in culture. These include, but are not limited to, thehybridoma technique, the human B-cell hybridoma technique, and theEBV-hybridoma technique (Kohler, G. et al. (1975) Nature 256:495-497;Kozbor, D. et al. (1985) J. Immunol. Methods 81:31-42; Cote, R. J. etal. (1983) Proc. Natl. Acad. Sci. USA 80:2026-2030; Cole, S. P. et al.(1984) Mol. Cell Biol. 62:109-120).

[0241] In addition, techniques developed for the production of “chimericantibodies,” such as the splicing of mouse antibody genes to humanantibody genes to obtain a molecule with appropriate antigen specificityand biological activity, can be used (Morrison, S. L. et al. (1984)Proc. Natd. Acad. Sci. USA 81:6851-6855; Neuberger, M. S. et al. (1984)Nature 312:604-608; Takeda, S. et al. (1985) Nature 314:452-454).Alternatively, techniques described for the production of single chainantibodies may be adapted, using methods known in the art, to produceVAP-specific single chain antibodies. Antibodies with relatedspecificity, but of distinct idiotypic composition, may be generated bychain shuffling from random combinatorial immunoglobulin libraries(Burton, D. R. (1991) Proc. Natl. Acad. Sci. USA 88:10134-10137).

[0242] Antibodies may also be produced by inducing in vivo production inthe lymphocyte population or by screening immunoglobulin libraries orpanels of highly specific binding reagents as disclosed in theliterature (Orlandi, R. et al. (1989) Proc. Natl. Acad. Sci. USA86:3833-3837; Winter, G. et al. (1991) Nature 349:293-299).

[0243] Antibody fragments which contain specific binding sites for VAPmay also be generated. For example, such fragments include, but are notlimited to, F(ab′)₂ fragments produced by pepsin digestion of theantibody molecule and Fab fragments generated by reducing the disulfidebridges of the F(ab)₂ fragments. Alternatively, Fab expression librariesmay be constructed to allow rapid and easy identification of monoclonalFab fragments with the desired specificity (Huse, W. D. et al. (1989)Science 246:1275-1281).

[0244] Various immunoassays may be used for screening to identifyantibodies having the desired specificity. Numerous protocols forcompetitive binding or immunoradiometric assays using either polyclonalor monoclonal antibodies with established specificities are well knownin the art. Such immunoassays typically involve the measurement ofcomplex formation between VAP and its specific antibody. A two-site,monoclonal-based immunoassay utilizing monoclonal antibodies reactive totwo non-interfering VAP epitopes is generally used, but a competitivebinding assay may also be employed (Pound, supra).

[0245] Various methods such as Scatchard analysis in conjunction withradioimmunoassay techniques may be used to assess the affinity ofantibodies for VAP. Affinity is expressed as an association constant,K_(a), which is defined as the molar concentration of VAP-antibodycomplex divided by the molar concentrations of free antigen and freeantibody under equilibrium conditions. The K_(a) determined for apreparation of polyclonal antibodies, which are heterogeneous in theiraffinities for multiple VAP epitopes, represents the average affinity,or avidity, of the antibodies for VAP. The K_(a) determined for apreparation of monoclonal antibodies, which are monospecific for aparticular VAP epitope, represents a true measure of affinity.High-affinity antibody preparations with K_(a) ranging from about 10⁹ to10¹² L/mole are preferred for use in immunoassays in which theVAP-antibody complex must withstand rigorous manipulations. Low-affinityantibody preparations with K_(a) ranging from about 106 to 107 L/moleare preferred for use in immunopurification and similar procedures whichultimately require dissociation of VAP, preferably in active form, fromthe antibody (Catty, D. (1988) Antibodies, Volume I: A PracticalApproach, IRL Press, Washington D.C.; Liddell, J. E. and A. Cryer (1991)A Practical Guide to Monoclonal Antibodies, John Wiley & Sons, New YorkN.Y.).

[0246] The titer and avidity of polyclonal antibody preparations may befurther evaluated to determine the quality and suitability of suchpreparations for certain downstream applications. For example, apolyclonal antibody preparation containing at least 1-2 mg specificantibody/ml, preferably 5-10 mg specific antibody/ml, is generallyemployed in procedures requiring precipitation of VAP-antibodycomplexes. Procedures for evaluating antibody specificity, titer, andavidity, and guidelines for antibody quality and usage in variousapplications, are generally available (Catty, supra; Coligan et al.,supra).

[0247] In another embodiment of the invention, polynucleotides encodingVAP, or any fragment or complement thereof, may be used for therapeuticpurposes. In one aspect, modifications of gene expression can beachieved by designing complementary sequences or antisense molecules(DNA, RNA, PNA, or modified oligonucleotides) to the coding orregulatory regions of the gene encoding VAP. Such technology is wellknown in the art, and antisense oligonucleotides or larger fragments canbe designed from various locations along the coding or control regionsof sequences encoding VAP (Agrawal, S., ed. (1996) AntisenseTherapeutics, Humana Press, Totawa N.J.).

[0248] In therapeutic use, any gene delivery system suitable forintroduction of the antisense sequences into appropriate target cellscan be used. Antisense sequences can be delivered intracellularly in theform of an expression plasmid which, upon transcription, produces asequence complementary to at least a portion of the cellular sequenceencoding the target protein (Slater, J. E. et al. (1998) J. AllergyClin. Immunol. 102:469-475; Scanlon, K. J. et al. (1995) 9:1288-1296).Antisense sequences can also be introduced intracellularly through theuse of viral vectors, such as retrovirus and adeno-associated virusvectors (Miller, A. D. (1990) Blood 76:271; Ausubel et al., supra;Uckert, W. and W. Walther (1994) Pharmacol. Ther. 63:323-347). Othergene delivery mechanisms include liposome-derived systems, artificialviral envelopes, and other systems known in the art (Rossi, J. J. (1995)Br. Med. Bull. 51:217-225; Boado, R. J. et al. (1998) J. Pharm. Sci.87:1308-1315; Morris, M. C. et al. (1997) Nucleic Acids Res.25:2730-2736).

[0249] In another embodiment of the invention, polynucleotides encodingVAP may be used for somatic or germline gene therapy. Gene therapy maybe performed to (i) correct a genetic deficiency (e.g., in the cases ofsevere combined immunodeficiency (SCID)-X1 disease characterized byX-linked inheritance (Cavazzana-Calvo, M. et al. (2000) Science288:669-672), severe combined immunodeficiency syndrome associated withan inherited adenosine deaminase (ADA) deficiency (Blaese, R. M. et al.(1995) Science 270:475480; Bordignon, C. et al. (1995) Science270:470-475), cystic fibrosis (Zabner, J. et al. (1993) Cell 75:207-216;Crystal, R. G. et al. (1995) Hum. Gene Therapy 6:643-666; Crystal, R. G.et al. (1995) Hum. Gene Therapy 6:667-703), thalassamias, familialhypercholesterolemia, and hemophilia resulting from Factor VR1 or FactorIX deficiencies (Crystal, R. G. (1995) Science 270:404-410; Verma, I. M.and N. Somia (1997) Nature 389:239-242)), (ii) express a conditionallylethal gene product (e.g., in the case of cancers which result fromunregulated cell proliferation), or (iii) express a protein whichaffords protection against intracellular parasites (e.g., against humanretroviruses, such as human immunodeficiency virus (HIV) (Baltimore, D.(1988) Nature 335:395-396; Poeschla, E. et al. (1996) Proc. Natl. Acad.Sci. USA 93:11395-11399), hepatitis B or C virus (HBV, HCV); fungalparasites, such as Candida albicans and Paracoccidioides brasiliensis;and protozoan parasites such as Plasmodium falciparum and Trypanosoniacruzi). In the case where a genetic deficiency in VAP expression orregulation causes disease, the expression of VAP from an appropriatepopulation of transduced cells may alleviate the clinical manifestationscaused by the genetic deficiency.

[0250] In a further embodiment of the invention, diseases or disorderscaused by deficiencies in VAP are treated by constructing mammalianexpression vectors encoding VAP and introducing these vectors bymechanical means into VAP-deficient cells. Mechanical transfertechnologies for use with cells iii vivo or ex vitro include (i) directDNA microinjection into individual cells, (ii) ballistic gold particledelivery, (iii) liposome-mediated transfection, (iv) receptor-mediatedgene transfer, and (v) the use of DNA transposons (Morgan, R. A. and W.F. Anderson (1993) Annu. Rev. Biochem. 62:191-217; Ivics, Z. (1997) Cell91:501-510; Boulay, J.-L. and H. Recipon (1998) Curr. Opin. Biotechnol.9:445-450).

[0251] Expression vectors that may be effective for the expression ofVAP include, but are not limited to, the PCDNA 3.1, EPITAG, PRCCMV2,PREP, PVAX, PCR2-TOPOTA vectors (Invitrogen, Carlsbad Calif.),PCMV-SCRIPT, PCMV-TAG, PEGSH/PERV (Stratagene, La Jolla Calif.), andPTET-OFF, PTET-ON, PTRE2, PTRE2-LUC, PTK-HYG (Clontech, Palo AltoCalif.). VAP may be expressed using (i) a constitutively activepromoter, (e.g., from cytomegalovirus (CMV), Rous sarcoma virus (RSV),SV40 virus, thymidine kinase (TK), or P-actin genes), (ii) an induciblepromoter (e.g., the tetracycline-regulated promoter (Gossen, M. and H.Bujard (1992) Proc. Natl. Acad. Sci. USA 89:5547-5551; Gossen, M. et al.(1995) Science 268:1766-1769; Rossi, F. M. V. and H. M. Blau (1998)Curr. Opin. Biotechnol. 9:451456), commercially available in the T-REXplasmid (Invitrogen)); the ecdysone-inducible promoter (available in theplasmids PVGRXR and PIND; Invitrogen); the FK506/rapamycin induciblepromoter; or the RU486/mifepristone inducible promoter (Rossi, F. M. V.and H. M. Blau, supra)), or (iii) a tissue-specific promoter or thenative promoter of the endogenous gene encoding VAP from a normalindividual.

[0252] Commercially available liposome transformation kits (e.g., thePERFECT LIPID TRANSFECTION KIT, available from Invitrogen) allow onewith ordinary skill in the art to deliver polynucleotides to targetcells in culture and require minimal effort to optimize experimentalparameters. In the alternative, transformation is performed using thecalcium phosphate method (Graham, F. L. and A. J. Eb (1973) Virology52:456467), or by electroporation (Neumann, E. et al. (1982) EMBO J.1:841-845). The introduction of DNA to primary cells requiresmodification of these standardized mammalian transfection protocols.

[0253] In another embodiment of the invention, diseases or disorderscaused by genetic defects with respect to VAP expression are treated byconstructing a retrovirus vector consisting of (i) the polynucleotideencoding VAP under the control of an independent promoter or theretrovirus long terminal repeat (LTR) promoter, (ii) appropriate RNApackaging signals, and (iii) a Rev-responsive element (RRE) along withadditional retrovirus cis-acting RNA sequences and coding sequencesrequired for efficient vector propagation. Retrovirus vectors (e.g., PFBand PFBNEO) are commercially available (Stratagene) and are based onpublished data (Riviere, I. et al. (1995) Proc. Natl. Acad. Sci. USA92:6733-6737), incorporated by reference herein. The vector ispropagated in an appropriate vector producing cell line (VPCL) thatexpresses an envelope gene with a tropism for receptors on the targetcells or a promiscuous envelope protein such as VSVg (Armentano, D. etal. (1987) J. Virol. 61:1647-1650; Bender, M. A. et al. (1987) J. Virol.61:1639-1646; Adam, M. A. and A. D. Miller (1988) J. Virol.62:3802-3806; Dull, T. et al. (1998) J. Virol. 72:8463-8471; Zufferey,R. et al. (1998) J. Virol. 72:9873-9880). U.S. Pat. No. 5,910,434 toRigg (“Method for obtaining retrovirus packaging cell lines producinghigh transducing efficiency retroviral supernatant”) discloses a methodfor obtaining retrovirus packaging cell lines and is hereby incorporatedby reference. Propagation of retrovirus vectors, transduction of apopulation of cells (e.g., CD4⁺ T-cells), and the return of transducedcells to a patient are procedures well known to persons skilled in theart of gene therapy and have been well documented (Ranga, U. et al.(1997) J. Virol. 71:7020-7029; Bauer, G. et al. (1997) Blood89:2259-2267; Bonyhadi, M. L. (1997) J. Virol. 71:47074716; Ranga, U. etal. (1998) Proc. Natl. Acad. Sci. USA 95:1201-1206; Su, L. (1997) Blood89:2283-2290).

[0254] In an embodiment, an adenovirus-based gene therapy deliverysystem is used to deliver polynucleotides encoding VAP to cells whichhave one or more genetic abnormalities with respect to the expression ofVAP. The construction and packaging of adenovirus-based vectors are wellknown to those with ordinary skill in the art. Replication defectiveadenovirus vectors have proven to be versatile for importing genesencoding immunoregulatory proteins into intact islets in the pancreas(Csete, M. E. et al. (1995) Transplantation 27:263-268). Potentiallyuseful adenoviral vectors are described in U.S. Pat. No. 5,707,618 toArmentano (“Adenovirus vectors for gene therapy”), hereby incorporatedby reference. For adenoviral vectors, see also Antinozzi, P. A. et al.(1999; Annu. Rev. Nutr. 19:511-544) and Verma, I. M. and N. Somia (1997;Nature 18:389:239-242).

[0255] In another embodiment, a herpes-based, gene therapy deliverysystem is used to deliver polynucleotides encoding VAP to target cellswhich have one or more genetic abnormalities with respect to theexpression of VAP. The use of herpes simplex virus (HSV)-based vectorsmay be especially valuable for introducing VAP to cells of the centralnervous system, for which HSV has a tropism. The construction andpackaging of herpes-based vectors are well known to those with ordinaryskill in the art. A replication-competent herpes simplex virus (HSV)type 1-based vector has been used to deliver a reporter gene to the eyesof primates (Liu, X. et al. (1999) Exp. Eye Res. 169:385-395). Theconstruction of a HSV-1 virus vector has also been disclosed in detailin U.S. Pat. No. 5,804,413 to DeLuca (“Herpes simplex virus strains forgene transfer”), which is hereby incorporated by reference. U.S. Pat.No. 5,804,413 teaches the use of recombinant HSV d92 which consists of agenome containing at least one exogenous gene to be transferred to acell under the control of the appropriate promoter for purposesincluding human gene therapy. Also taught by this patent are theconstruction and use of recombinant HSV strains deleted for ICP4, ICP27and ICP22. For HSV vectors, see also Goins, W. F. et al. (1999; J.Virol. 73:519-532) and Xu, H. et al. (1994; Dev. Biol. 163:152-161). Themanipulation of cloned herpesvirus sequences, the generation ofrecombinant virus following the transfection of multiple plasmidscontaining different segments of the large herpesvirus genomes, thegrowth and propagation of herpesvirus, and the infection of cells withherpesvirus are techniques well known to those of ordinary skill in theart.

[0256] In another embodiment, an alphavirus (positive, single-strandedRNA virus) vector is used to deliver polynucleotides encoding VAP totarget cells. The biology of the prototypic alphavirus, Sernliki ForestVirus (SFV), has been studied extensively and gene transfer vectors havebeen based on the SFV genome (Garoff, H. and K.-J. Li (1998) Curr. Opin.Biotechnol. 9:464-469). During alphavirus RNA replication, a subgenomicRNA is generated that normnally encodes the viral capsid proteins. Thissubgenomic RNA replicates to higher levels than the full length genomicRNA, resulting in the overproduction of capsid proteins relative to theviral proteins with enzymatic activity (e.g., protease and polymerase).Similarly, inserting the coding sequence for VAP into the alphavirusgenome in place of the capsid-coding region results in the production ofa large number of VAP-coding RNAs and the synthesis of high levels ofVAP in vector transduced cells. While alphavirus infection is typicallyassociated with cell lysis within a few days, the ability to establish apersistent infection in harnster normal kidney cells (BHK-21) with avariant of Sindbis virus (SIN) indicates that the lytic replication ofalphaviruses can be altered to suit the needs of the gene therapyapplication (Dryga, S. A. et al. (1997) Virology 228:74-83). The widehost range of alphaviruses will allow the introduction of VAP into avariety of cell types. The specific transduction of a subset of cells ina population may require the sorting of cells prior to transduction. Themethods of manipulating infectious cDNA clones of alphaviruses,performing alphavirus cDNA and RNA transfections, and performingalphavirus infections, are well known to those with ordinary skill inthe art.

[0257] Oligonucleotides derived from the transcription initiation site,e.g., between about positions −10 and +10 from the start site, may alsobe employed to inhibit gene expression. Similarly, inhibition can beachieved using triple helix base-pairing methodology. Triple helixpairing is useful because it causes inhibition of the ability of thedouble helix to open sufficiently for the binding of polymerases,transcription factors, or regulatory molecules. Recent therapeuticadvances using triplex DNA have been described in the literature (Gee,J. E. et al. (1994) in Huber, B. E. and B. I. Carr, Molecular andImmunologic Approaches, Futura Publishing, Mt. Kisco N.Y., pp. 163-177).A complementary sequence or antisense molecule may also be designed toblock translation of mRNA by preventing the transcript from binding toribosomes.

[0258] Ribozymes, enzymatic RNA molecules, may also be used to catalyzethe specific cleavage of RNA. The mechanism of ribozyme action involvessequence-specific hybridization of the ribozyme molecule tocomplementary target RNA, followed by endonucleolytic cleavage. Forexample, engineered hammerhead motif ribozyme molecules may specificallyand efficiently catalyze endonucleolytic cleavage of RNA moleculesencoding VAP.

[0259] Specific ribozyme cleavage sites within any potential RNA targetare initially identified by scanning the target molecule for ribozymecleavage sites, including the following sequences: GUA, GUU, and GUC.Once identified, short RNA sequences of between 15 and 20ribonucleotides, corresponding to the region of the target genecontaining the cleavage site, may be evaluated for secondary structuralfeatures which may render the oligonucleotide inoperable. Thesuitability of candidate targets may also be evaluated by testingaccessibility to hybridization with complementary oligonucleotides usingribonuclease protection assays.

[0260] Complementary ribonucleic acid molecules and ribozymes may beprepared by any method known in the art for the synthesis of nucleicacid molecules. These include techniques for chemically synthesizingoligonucleotides such as solid phase phosphoramidite chemical synthesis.Alternatively, RNA molecules may be generated by in vitro and in vivotranscription of DNA molecules encoding VAP. Such DNA sequences may beincorporated into a wide variety of vectors with suitable RNA polymerasepromoters such as T7 or SP6. Alternatively, these cDNA constructs thatsynthesize complementary RNA, constitutively or inducibly, can beintroduced into cell lines, cells, or tissues.

[0261] RNA molecules may be modified to increase intracellular stabilityand half-life. Possible modifications include, but are not limited to,the addition of flanking sequences at the 5′ and/or 3′ ends of themolecule, or the use of phosphorothioate or 2′ O-methyl rather thanphosphodiesterase linkages within the backbone of the molecule. Thisconcept is inherent in the production of PNAs and can be extended in allof these molecules by the inclusion of nontraditional bases such asinosine, queosine, and wybutosine, as well as acetyl-, methyl-, thio-,and similarly modified forms of adenine, cytidine, guanine, thymine, anduridine which are not as easily recognized by endogenous endonucleases.

[0262] In other embodiments of the invention, the expression of one ormore selected polynucleotides of the present invention can be altered,inhibited, decreased, or silenced using RNA interference (RNAI) orpost-transcriptional gene silencing (PTGS) methods known in the art.RNAi is a post-transcriptional mode of gene silencing in whichdouble-stranded RNA (dsRNA) introduced into a targeted cell specificallysuppresses the expression of the homologous gene (i.e., the gene bearingthe sequence complementary to the dsRNA). This effectively knocks out orsubstantially reduces the expression of the targeted gene. PTGS can alsobe accomplished by use of DNA or DNA fragments as well. RNAi methods aredescribed by Fire, A. et al. (1998; Nature 391:806-811) and Gura, T.(2000; Nature 404:804-808). PTGS can also be initiated by introductionof a complementary segment of DNA into the selected tissue using genedelivery and/or viral vector delivery methods described herein or knownin the art.

[0263] RNAi can be induced in marnmalian cells by the use of smallinterfering RNA also known as siRNA. SiRNA are shorter segments of dsRNA(typically about 21 to 23 nucleotides in length) that result in vivofrom cleavage of introduced dsRNA by the action of an endogenousribonuclease. SiRNA appear to be the mediators of the RNAi effect inmammals. The most effective siRNAs appear to be 21 nucleotide dsRNAswith 2 nucleotide 3′ overhangs. The use of siRNA for inducing RNAi inmammalian cells is described by Elbashir, S. M. et al. (2001; Nature411:494-498).

[0264] SiRNA can either be generated indirectly by introduction of dsRNAinto the targeted cell, or directly by mammalian transfection methodsand agents described herein or known in the art (such asliposome-mediated transfection, viral vector methods, or otherpolynucleotide delivery/introductory methods). Suitable SiRNAs can beselected by examining a transcript of the target polynucleotide (e.g.,mRNA) for nucleotide sequences downstream from the AUG start codon andrecording the occurrence of each nucleotide and the 3′ adjacent 19 to 23nucleotides as potential siRNA target sites, with sequences having a 21nucleotide length being preferred. Regions to be avoided for targetsiRNA sites include the 5′ and 3′ untranslated regions (UTRs) andregions near the start codon (within 75 bases), as these may be richerin regulatory protein binding sites. UTR-binding proteins and/ortranslation initiation complexes may interfere with binding of the siRNPendonuclease complex. The selected target sites for siRNA can then becompared to the appropriate genome database (e.g., human, etc.) usingBLAST or other sequence comparison algorithms known in the art. Targetsequences with significant homology to other coding sequences can beeliminated from consideration. The selected SiRNAs can be produced bychemical synthesis methods known in the art or by in vitro transcriptionusing commercially available methods and kits such as the SILENCER siRNAconstruction kit (Ambion, Austin Tex.).

[0265] In alternative embodiments, long-term gene silencing and/or RNAieffects can be induced in selected tissue using expression vectors thatcontinuously express siRNA. This can be accomplished using expressionvectors that are engineered to express hairpin RNAs (shRNAs) usingmethods known in the art (see, e.g., Brurnmelkamp, T. R. et al. (2002)Science 296:550-553; and Paddison, P. J. et al. (2002) Genes Dev.16:948-958). In these and related embodiments, shRNAs can be deliveredto target cells using expression vectors known in the art. An example ofa suitable expression vector for delivery of siRNA is thePSILENCER1.0-U6 (circular) plasmid (Ambion). Once delivered to thetarget tissue, shRNAs are processed in vivo into siRNA-like moleculescapable of carrying out gene-specific silencing.

[0266] In various embodiments, the expression levels of genes targetedby RNAi or PTGS methods can be determined by assays for mRNA and/orprotein analysis. Expression levels of the mRNA of a targeted gene, canbe determined by northern analysis methods using, for example, theNORTHERNMAX-GLY kit (Ambion); by microarray methods; by PCR methods; byreal time PCR methods; and by other RNA/polynucleotide assays known inthe art or described herein. Expression levels of the protein encoded bythe targeted gene can be determined by Western analysis using standardtechniques known in the art.

[0267] An additional embodiment of the invention encompasses a methodfor screening for a compound which is effective in altering expressionof a polynucleotide encoding VAP. Compounds which may be effective inaltering expression of a specific polynucleotide may include, but arenot limited to, oligonucleotides, antisense oligonucleotides, triplehelix-forming oligonucleotides, transcription factors and otherpolypeptide transcriptional regulators, and non-macromolecular chemicalentities which are capable of interacting with specific polynucleotidesequences. Effective compounds may alter polynucleotide expression byacting as either inhibitors or promoters of polynucleotide expression.Thus, in the treatment of disorders associated with increased VAPexpression or activity, a compound which specifically inhibitsexpression of the polynucleotide encoding VAP may be therapeuticallyuseful, and in the treatment of disorders associated with decreased VAPexpression or activity, a compound which specifically promotesexpression of the polynucleotide encoding VAP may be therapeuticallyuseful.

[0268] In various embodiments, one or more test compounds may bescreened for effectiveness in altering expression of a specificpolynucleotide. A test compound may be obtained by any method commonlyknown in the art, including chemical modification of a compound known tobe effective in altering polynucleotide expression; selection from anexisting, commercially-available or proprietary library ofnaturally-occurring or non-natural chemical compounds; rational designof a compound based on chemical and/or structural properties of thetarget polynucleotide; and selection from a library of chemicalcompounds created combinatorially or randomly. A sample comprising apolynucleotide encoding VAP is exposed to at least one test compoundthus obtained. The sample may comprise, for example, an intact orpermeabilized cell, or an in vitro cell-free or reconstitutedbiochemical system. Alterations in the expression of a polynucleotideencoding VAP are assayed by any method commonly known in the art.Typically, the expression of a specific nucleotide is detected byhybridization with a probe having a nucleotide sequence complementary tothe sequence of the polynucleotide encoding VAP. The amount ofhybridization may be quantified, thus forming the basis for a comparisonof the expression of the polynucleotide both with and without exposureto one or more test compounds. Detection of a change in the expressionof a polynucleotide exposed to a test compound indicates that the testcompound is effective in altering the expression of the polynucleotide.A screen for a compound effective in altering expression of a specificpolynucleotide can be carried out, for example, using aSchizosaccharomyces pombe gene expression system (Atkins, D. et al.(1999) U.S. Pat. No. 5,932,435; Arndt, G. M. et al. (2000) Nucleic AcidsRes. 28:E15) or a human cell line such as HeLa cell (Clarke, M. L. etal. (2000) Biochem. Biophys. Res. Commun. 268:8-13). A particularembodiment of the present invention involves screening a combinatoriallibrary of oligonucleotides (such as deoxyribonucleotides,ribonucleotides, peptide nucleic acids, and modified oligonucleotides)for antisense activity against a specific polynucleotide sequence(Bruice, T. W. et al. (1997) U.S. Pat. No. 5,686,242; Bruice, T. W. etal. (2000) U.S. Pat. No. 6,022,691).

[0269] Many methods for introducing vectors into cells or tissues areavailable and equally suitable for use in vivo, in vitro, and ex vivo.For ex vivo therapy, vectors may be introduced into stem cells takenfrom the patient and clonally propagated for autologous transplant backinto that same patient. Delivery by transfection, by liposomeinjections, or by polycationic amino polymers may be achieved usingmethods which are well known in the art (Goldman, C. K. et al. (1997)Nat. Biotechnol. 15:462-466).

[0270] Any of the therapeutic methods described above may be applied toany subject in need of such therapy, including, for example, mammalssuch as humans, dogs, cats, cows, horses, rabbits, and monkeys.

[0271] An additional embodiment of the invention relates to theadministration of a composition which generally comprises an activeingredient formulated with a pharmaceutically acceptable excipient.Excipients may include, for example, sugars, starches, celluloses, gums,and proteins. Various formulations are commonly known and are thoroughlydiscussed in the latest edition of Remington's Pharmaceutical Sciences(Maack Publishing, Easton Pa.). Such compositions may consist of VAP,antibodies to VAP, and mimetics, agonists, antagonists, or inhibitors ofVAP.

[0272] In various embodiments, the compositions described herein, suchas pharmaceutical compositions, may be administered by any number ofroutes including, but not limited to, oral, intravenous, intramuscular,intra-arterial, intramedullary, intrathecal, intraventricular,pulmonary, transdermal, subcutaneous, intraperitoneal, intranasal,enteral, topical, sublingual, or rectal means.

[0273] Compositions for pulmonary administration may be prepared inliquid or dry powder form. These compositions are generally aerosolizedimmediately prior to inhalation by the patient. In the case of smallmolecules (e.g. traditional low molecular weight organic drugs), aerosoldelivery of fast-acting formulations is well-known in the art. In thecase of macromolecules (e.g. larger peptides and proteins), recentdevelopments in the field of pulmonary delivery via the alveolar regionof the lung have enabled the practical delivery of drugs such as insulinto blood circulation (see, e.g., Patton, J. S. et al., U.S. Pat. No.5,997,848). Pulmonary delivery allows administration without needleinjection, and obviates the need for potentially toxic penetrationenhancers.

[0274] Compositions suitable for use in the invention includecompositions wherein the active ingredients are contained in aneffective amount to achieve the intended purpose. The determination ofan effective dose is well within the capability of those skilled in theart.

[0275] Specialized forms of compositions may be prepared for directintracellular delivery of macromolecules comprising VAP or fragmentsthereof. For example, liposome preparations containing acell-impermeable macromolecule may promote cell fusion and intracellulardelivery of the macromolecule. Alternatively, VAP or a fragment thereofmay be joined to a short cationic N-terminal portion from the HEV Tat-1protein. Fusion proteins thus generated have been found to transduceinto the cells of all tissues, including the brain, in a mouse modelsystem (Schwarze, S. R. et al. (1999) Science 285:1569-1572).

[0276] For any compound, the therapeutically effective dose can beestimated initially either in cell culture assays, e.g., of neoplasticcells, or in animal models such as mice, rats, rabbits, dogs, monkeys,or pigs. An animal model may also be used to determine the appropriateconcentration range and route of administration. Such information canthen be used to determine useful doses and routes for administration inhumans.

[0277] A therapeutically effective dose refers to that amount of activeingredient, for example VAP or fragments thereof, antibodies of VAP, andagonists, antagonists or inhibitors of VAP, which ameliorates thesymptoms or condition. Therapeutic efficacy and toxicity may bedetermined by standard pharmaceutical procedures in cell cultures orwith experimental animals, such as by calculating the ED₅₀ (the dosetherapeutically effective in 50% of the population) or LD₅₀ (the doselethal to 50% of the population) statistics. The dose ratio of toxic totherapeutic effects is the therapeutic index, which can be expressed asthe LD₅₀/ED₅₀ ratio. Compositions which exhibit large therapeuticindices are preferred. The data obtained from cell culture assays andanimal studies are used to formulate a range of dosage for human use.The dosage contained in such compositions is preferably within a rangeof circulating concentrations that includes the ED₅₀ with little or notoxicity. The dosage varies within this range depending upon the dosageform employed, the sensitivity of the patient, and the route ofadministration.

[0278] The exact dosage will be determined by the practitioner, in lightof factors related to the subject requiring treatment. Dosage andadministration are adjusted to provide sufficient levels of the activemoiety or to maintain the desired effect. Factors which may be takeninto account include the severity of the disease state, the generalhealth of the subject, the age, weight, and gender of the subject, timeand frequency of administration, drug combination(s), reactionsensitivities, and response to therapy. Long-acting compositions may beadministered every 3 to 4 days, every week, or biweekly depending on thehalf-life and clearance rate of the particular formulation.

[0279] Normal dosage amounts may vary from about 0.1 μg to 100,000 μg,up to a total dose of about 1 gram, depending upon the route ofadministration. Guidance as to particular dosages and methods ofdelivery is provided in the literature and generally available topractitioners in the art. Those skilled in the art will employ differentformulations for nucleotides than for proteins or their inhibitors.Similarly, delivery of polynucleotides or polypeptides will be specificto particular cells, conditions, locations, etc.

[0280] Diagnostics

[0281] In another embodiment, antibodies which specifically bind VAP maybe used for the diagnosis of disorders characterized by expression ofVAP, or in assays to monitor patients being treated with VAP oragonists, antagonists, or inhibitors of VAP. Antibodies useful fordiagnostic purposes may be prepared in the same manner as describedabove for therapeutics. Diagnostic assays for VAP include methods whichutilize the antibody and a label to detect VAP in human body fluids orin extracts of cells or tissues. The antibodies may be used with orwithout modification, and may be labeled by covalent or non-covalentattachment of a reporter molecule. A wide variety of reporter molecules,several of which are described above, are known in the art and may beused.

[0282] A variety of protocols for measuring VAP, including ELISAs, RIAs,and FACS, are known in the art and provide a basis for diagnosingaltered or abnormal levels of VAP expression. Normal or standard valuesfor VAP expression are established by combining body fluids or cellextracts taken from normal mammalian subjects, for example, humansubjects, with antibodies to VAP under conditions suitable for complexformation. The amount of standard complex formation may be quantitatedby various methods, such as photometric means. Quantities of VAPexpressed in subject, control, and disease samples from biopsied tissuesare compared with the standard values. Deviation between standard andsubject values establishes the parameters for diagnosing disease.

[0283] In another embodiment of the invention, polynucleotides encodingVAP may be used for diagnostic purposes. The polynucleotides which maybe used include oligonucleotides, complementary RNA and DNA molecules,and PNAs. The polynucleotides may be used to detect and quantify geneexpression in biopsied tissues in which expression of VAP may becorrelated with disease. The diagnostic assay may be used to determineabsence, presence, and excess expression of VAP, and to monitorregulation of VAP levels during therapeutic intervention.

[0284] In one aspect, hybridization with PCR probes which are capable ofdetecting polynucleotides, including genomic sequences, encoding VAP orclosely related molecules may be used to identify nucleic acid sequenceswhich encode VAP. The specificity of the probe, whether it is made froma highly specific region, e.g., the 5′ regulatory region, or from a lessspecific region, e.g., a conserved motif, and the stringency of thehybridization or amplification will determine whether the probeidentifies only naturally occurring sequences encoding VAP, allelicvariants, or related sequences.

[0285] Probes may also be used for the detection of related sequences,and may have at least 50% sequence identity to any of the VAP encodingsequences. The hybridization probes of the subject invention may be DNAor RNA and may be derived from the sequence of SEQ ID NO:21-40 or fromgenomic sequences including promoters, enhancers, and introns of the VAPgene.

[0286] Means for producing specific hybridization probes forpolynucleotides encoding VAP include the cloning of polynucleotidesencoding VAP or VAP derivatives into vectors for the production of mRNAprobes. Such vectors are known in the art, are commercially available,and may be used to synthesize RNA probes in vitro by means of theaddition of the appropriate RNA polymerases and the appropriate labelednucleotides. Hybridization probes may be labeled by a variety ofreporter groups, for example, by radionuclides such as ³²P or ³⁵S, or byenzymatic labels, such as alkaline phosphatase coupled to the probe viaavidinhbiotin coupling systems, and the like.

[0287] Polynucleotides encoding VAP may be used for the diagnosis ofdisorders associated with expression of VAP. Examples of such disordersinclude, but are not limited to, a vesicle trafficking disorder, such ascystic fibrosis, glucose-galactose malabsorption syndrome,hypercholesterolemia, diabetes mellitus, diabetes insipidus, hyper- andhypoglycemia, Grave's disease, goiter, Cushing's disease, and Addison'sdisease, gastrointestinal disorders including ulcerative colitis,gastric and duodenal ulcers, other conditions associated with abnormalvesicle trafficking, including acquired immunodeficiency syndrome(AIDS), allergies including hay fever, asthma, and urticaria (hives),autoimmune hemolytic anemia, proliferative glomerulonephritis,inflammatory bowel disease, multiple sclerosis, myasthenia gravis,rheumatoid and osteoarthritis, scleroderma, Chediak-Higashi andSjogren's syndromes, systemic lupus erythematosus, toxic shock syndrome,traumatic tissue damage, and viral, bacterial, fungal, helminthic, andprotozoal infections, an autoimmune/inflammatory disorder, such asacquired immunodeficiency syndrome (AIDS), Addison's disease, adultrespiratory distress syndrome, allergies, ankylosing spondylitis,amyloidosis, anemia, asthma, atherosclerosis, autoinmmune hemolyticanemia, autoimmune thyroiditis, autoimmunepolyendocrinopathy-candidiasis-ectodermal dystrophy (APECED),bronchitis, cholecystitis, contact ermatitis, Crohn's disease, atopicdermatitis, dermatomyositis, diabetes mellitus, emphysema, pisodiclymphopenia with lymphocytotoxins, erythroblastosis fetalis, erythemanodosum, atrophic astritis, glomerulonephritis, Goodpasture's syndrome,gout, Graves' disease, Hashimoto's hyroiditis, hypereosinophilia,irritable bowel syndrome, multiple sclerosis, myasthenia gravis,myocardial or pericardial inflammation, osteoarthritis, osteoporosis,pancreatitis, polymyositis, psoriasis, Reiter's syndrome, rheumatoidarthritis, scleroderma, Sjogren's syndrome, systemic anaphylaxis,systemic lupus erythematosus, systemic sclerosis, thrombocytopenicpurpura, ulcerative colitis, uveitis, Werner syndrome, complications ofcancer, hemodialysis, and extracorporeal circulation, viral, bacterial,fungal, parasitic, protozoal, and helninthic infections, and trauma; anda cancer, such as adenocarcinoma, leukemia, lymphoma, melanoma, myeloma,sarcoma, teratocarcinoma, and, in particular, cancers of the adrenalgland, bladder, bone, bone marrow, brain, breast, cervix, colon, gallbladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung,muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands,skin, spleen, testis, thymus, thyroid, and uterus. Polynucleotidesencoding VAP may be used in Southern or northern analysis, dot blot, orother membrane-based technologies; in PCR technologies; in dipstick,pin, and multiformat ELISA-like assays; and in microarrays utilizingfluids or tissues from patients to detect altered VAP expression. Suchqualitative or quantitative methods are well known in the art.

[0288] In a particular embodiment, polynucleotides encoding VAP may beused in assays that detect the presence of associated disorders,particularly those mentioned above. Polynucleotides complementary tosequences encoding VAP may be labeled by standard methods and added to afluid or tissue sample from a patient under conditions suitable for theformation of hybridization complexes. After a suitable incubationperiod, the sample is washed and the signal is quantified and comparedwith a standard value. If the amount of signal in the patient sample issignificantly altered in comparison to a control sample then thepresence of altered levels of polynucleotides encoding VAP in the sampleindicates the presence of the associated disorder. Such assays may alsobe used to evaluate the efficacy of a particular therapeutic treatmentregimen in animal studies, in clinical trials, or to monitor thetreatment of an individual patient.

[0289] In order to provide a basis for the diagnosis of a disorderassociated with expression of VAP, a normal or standard profile forexpression is established. This may be accomplished by combining bodyfluids or cell extracts taken from normal subjects, either animal orhuman, with a sequence, or a fragment thereof, encoding VAP, underconditions suitable for hybridization or amplification. Standardhybridization may be quantified by comparing the values obtained fromnormal subjects with values from an experiment in which a known amountof a substantially purified polynucleotide is used. Standard valuesobtained in this manner may be compared with values obtained fromsamples from patients who are symptomatic for a disorder. Deviation fromstandard values is used to establish the presence of a disorder.

[0290] Once the presence of a disorder is established and a treatmentprotocol is initiated, hybridization assays may be repeated on a regularbasis to determine if the level of expression in the patient begins toapproximate that which is observed in the normal subject. The resultsobtained from successive assays may be used to show the efficacy oftreatment over a period ranging from several days to months.

[0291] With respect to cancer, the presence of an abnormal amount oftranscript (either under- or overexpressed) in biopsied tissue from anindividual may indicate a predisposition for the development of thedisease, or may provide a means for detecting the disease prior to theappearance of actual clinical symptoms. A more definitive diagnosis ofthis type may allow health professionals to employ preventative measuresor aggressive treatment earlier, thereby preventing the development orfurther progression of the cancer.

[0292] Additional diagnostic uses for oligonucleotides designed from thesequences encoding VAP may involve the use of PCR. These oligomers maybe chemically synthesized, generated enzymatically, or produced invitro. Oligomers will preferably contain a fragment of a polynucleotideencoding VAP, or a fragment of a polynucleotide complementary to thepolynucleotide encoding VAP, and will be employed under optimizedconditions for identification of a specific gene or condition. Oligomersmay also be employed under less stringent conditions for detection orquantification of closely related DNA or RNA sequences.

[0293] In a particular aspect, oligonucleotide primers derived frompolynucleotides encoding VAP may be used to detect single nucleotidepolymorphisms (SNPs). SNPs are substitutions, insertions and deletionsthat are a frequent cause of inherited or acquired genetic disease inhumans. Methods of SNP detection include, but are not limited to,single-stranded conformation polymorphism (SSCP) and fluorescent SSCP(fSSCP) methods. In SSCP, oligonucleotide primers derived frompolynucleotides encoding VAP are used to amplify DNA using thepolymerase chain reaction (PCR). The DNA may be derived, for example,from diseased or normal tissue, biopsy samples, bodily fluids, and thelike. SNPs in the DNA cause differences in the secondary and tertiarystructures of PCR products in single-stranded form, and thesedifferences are detectable using gel electrophoresis in non-denaturinggels. In fSCCP, the oligonucleotide primers are fluorescently labeled,which allows detection of the amplimers in high-throughput equipmentsuch as DNA sequencing machines. Additionally, sequence databaseanalysis methods, termed in silico SNP (is SNP), are capable ofidentifying polymorphisms by comparing the sequence of individualoverlapping DNA fragments which assemble into a common consensussequence. These computer-based methods filter out sequence variationsdue to laboratory preparation of DNA and sequencing errors usingstatistical models and automated analyses of DNA sequence chromatograms.In the alternative, SNPs may be detected and characterized by massspectrometry using, for example, the high throughput MASSARRAY system(Sequenom, Inc., San Diego Calif.).

[0294] SNPs may be used to study the genetic basis of human disease. Forexample, at least 16 common SNPs have been associated withnon-insulin-dependent diabetes mellitus. SNPs are also useful forexamining differences in disease outcomes in monogenic disorders, suchas cystic fibrosis, sickle cell anemia, or chronic granulomatousdisease. For example, variants in the mannose-binding lectin, MBL2, havebeen shown to be correlated with deleterious pulmonary outcomes incystic fibrosis. SNPs also have utility in pharmacogenomics, theidentification of genetic variants that influence a patient's responseto a drug, such as life-threatening toxicity. For example, a variationin N-acetyl transferase is associated with a high incidence ofperipheral neuropathy in response to the anti-tuberculosis drugisoniazid, while a variation in the core promoter of the ALOX5 generesults in diminished clinical response to treatment with an anti-asthmadrug that targets the 5-lipoxygenase pathway. Analysis of thedistribution of SNPs in different populations is useful forinvestigating genetic drift, mutation, recombination, and selection, aswell as for tracing the origins of populations and their migrations(Taylor, J. G. et al. (2001) Trends Mol. Med. 7:507-512; Kwok, P.-Y. andZ. Gu (1999) Mol. Med. Today 5:538-543; Nowotny, P. et al. (2001) Curr.Opin. Neurobiol. 11:637-641).

[0295] Methods which may also be used to quantify the expression of VAPinclude radiolabeling or biotinylating nucleotides, coamplification of acontrol nucleic acid, and interpolating results from standard curves(Melby, P. C. et al. (1993) J. Immunol. Methods 159:235-244; Duplaa, C.et al. (1993) Anal. Biochem. 212:229-236). The speed of quantitation ofmultiple samples may be accelerated by running the assay in ahigh-throughput format where the oligomer or polynucleotide of interestis presented in various dilutions and a spectrophotometric orcolorimetric response gives rapid quantitation.

[0296] In further embodiments, oligonucleotides or longer fragmentsderived from any of the polynucleotides described herein may be used aselements on a microarray. The microarray can be used in transcriptimaging techniques which monitor the relative expression levels of largenumbers of genes simultaneously as described below. The microarray mayalso be used to identify genetic variants, mutations, and polymorphisms.This information may be used to determine gene function, to understandthe genetic basis of a disorder, to diagnose a disorder, to monitorprogression/regression of disease as a function of gene expression, andto develop and monitor the activities of therapeutic agents in thetreatment of disease. In particular, this information may be used todevelop a pharmacogenomic profile of a patient in order to select themost appropriate and effective treatment regimen for that patient. Forexample, therapeutic agents which are highly effective and display thefewest side effects may be selected for a patient based on his/herpharmacogenomic profile.

[0297] In another embodiment, VAP, fragments of VAP, or antibodiesspecific for VAP may be used as elements on a microarray. The microarraymay be used to monitor or measure protein-protein interactions,drug-target interactions, and gene expression profiles, as describedabove.

[0298] A particular embodiment relates to the use of the polynucleotidesof the present invention to generate a transcript image of a tissue orcell type. A transcript image represents the global pattern of geneexpression by a particular tissue or cell type. Global gene expressionpatterns are analyzed by quantifying the number of expressed genes andtheir relative abundance under given conditions and at a given time(Seilhamer et al., “Comparative Gene Transcript Analysis,” U.S. Pat. No.5,840,484; hereby expressly incorporated by reference herein). Thus atranscript image may be generated by hybridizing the polynucleotides ofthe present invention or their complements to the totality oftranscripts or reverse transcripts of a particular tissue or cell type.In one embodiment, the hybridization takes place in high-throughputformat, wherein the polynucleotides of the present invention or theircomplements comprise a subset of a plurality of elements on amicroarray. The resultant transcript image would provide a profile ofgene activity.

[0299] Transcript images may be generated using transcripts isolatedfrom tissues, cell lines, biopsies, or other biological samples. Thetranscript image may thus reflect gene expression in vivo, as in thecase of a tissue or biopsy sample, or in vitro, as in the case of a cellline.

[0300] Transcript images which profile the expression of thepolynucleotides of the present invention may also be used in conjunctionwith in vitro model systems and preclinical evaluation ofpharmaceuticals, as well as toxicological testing of industrial andnaturally-occurring environmental compounds. All compounds inducecharacteristic gene expression patterns, frequently termed molecularfingerprints or toxicant signatures, which are indicative of mechanismsof action and toxicity (Nuwaysir, E. F. et al. (1999) Mol. Carcinog.24:153-159; Steiner, S. and N. L. Anderson (2000) Toxicol. Lett.112-113:467471). If a test compound has a signature similar to that of acompound with known toxicity, it is likely to share those toxicproperties. These fingerprints or signatures are most useful and refinedwhen they contain expression information from a large number of genesand gene families. Ideally, a genome-wide measurement of expressionprovides the highest quality signature. Even genes whose expression isnot altered by any tested compounds are important as well, as the levelsof expression of these genes are used to normalize the rest of theexpression data. The normalization procedure is useful for comparison ofexpression data after treatment with different compounds. While theassignment of gene function to elements of a toxicant signature aids ininterpretation of toxicity mechanisms, knowledge of gene function is notnecessary for the statistical matching of signatures which leads toprediction of toxicity (see, for example, Press Release 00-02 from theNational Institute of Environmental Health Sciences, released Feb. 29,2000, available at http://www.niehs.nih.gov/oc/news/toxchip.htm).Therefore, it is important and desirable in toxicological screeningusing toxicant signatures to include all expressed gene sequences.

[0301] In an embodiment, the toxicity of a test compound can be assessedby treating a biological sample containing nucleic acids with the testcompound. Nucleic acids that are expressed in the treated biologicalsample are hybridized with one or more probes specific to thepolynucleotides of the present invention, so that transcript levelscorresponding to the polynucleotides of the present invention may bequantified. The transcript levels in the treated biological sample arecompared with levels in an untreated biological sample. Differences inthe transcript levels between the two samples are indicative of a toxicresponse caused by the test compound in the treated sample.

[0302] Another embodiment relates to the use of the polypeptidesdisclosed herein to analyze the proteome of a tissue or cell type. Theterm proteome refers to the global pattern of protein expression in aparticular tissue or cell type. Each protein component of a proteome canbe subjected individually to further analysis. Proteome expressionpatterns, or profiles, are analyzed by quantifying the number ofexpressed proteins and their relative abundance under given conditionsand at a given time. A profile of a cell's proteome may thus begenerated by separating and analyzing the polypeptides of a particulartissue or cell type. In one embodiment, the separation is achieved usingtwo-dimensional gel electrophoresis, in which proteins from a sample areseparated by isoelectric focusing in the first dimension, and thenaccording to molecular weight by sodium dodecyl sulfate slab gelelectrophoresis in the second dimension (Steiner and Anderson, supra).The proteins are visualized in the gel as discrete and uniquelypositioned spots, typically by staining the gel with an agent such asCoomassie Blue or silver or fluorescent stains. The optical density ofeach protein spot is generally proportional to the level of the proteinin the sample. The optical densities of equivalently positioned proteinspots from different samples, for example, from biological sampleseither treated or untreated with a test compound or therapeutic agent,are compared to identify any changes in protein spot density related tothe treatment. The proteins in the spots are partially sequenced using,for example, standard methods employing chemical or enzymatic cleavagefollowed by mass spectrometry. The identity of the protein in a spot maybe determined by comparing its partial sequence, preferably of at least5 contiguous amino acid residues, to the polypeptide sequences ofinterest. In some cases, further sequence data may be obtained fordefinitive protein identification.

[0303] A proteomic profile may also be generated using antibodiesspecific for VAP to quantify the levels of VAP expression. In oneembodiment, the antibodies are used as elements on a microarray, andprotein expression levels are quantified by exposing the microarray tothe sample and detecting the levels of protein bound to each arrayelement (Lueling, A. et al. (1999) Anal. Biochem. 270:103-111; Mendoze,L. G. et al. (1999) Biotechniques 27:778-788). Detection may beperformed by a variety of methods known in the art, for example, byreacting the proteins in the sample with a thiol- or amino-reactivefluorescent compound and detecting the amount of fluorescence bound ateach array element.

[0304] Toxicant signatures at the proteome level are also useful fortoxicological screening, and should be analyzed in parallel withtoxicant signatures at the transcript level. There is a poor correlationbetween transcript and protein abundances for some proteins in sometissues (Anderson, N. L. and J. Seilhamer (1997) Electrophoresis18:533-537), so proteome toxicant signatures may be useful in theanalysis of compounds which do not significantly affect the transcriptimage, but which alter the proteomic profile. In addition, the analysisof transcripts in body fluids is difficult, due to rapid degradation ofmRNA, so proteomic profiling may be more reliable and informative insuch cases.

[0305] In another embodiment, the toxicity of a test compound isassessed by treating a biological sample containing proteins with thetest compound. Proteins that are expressed in the treated biologicalsample are separated so that the amount of each protein can bequantified. The amount of each protein is compared to the amount of thecorresponding protein in an untreated biological sample. A difference inthe amount of protein between the two samples is indicative of a toxicresponse to the test compound in the treated sample. Individual proteinsare identified by sequencing the amino acid residues of the individualproteins and comparing these partial sequences to the polypeptides ofthe present invention.

[0306] In another embodiment, the toxicity of a test compound isassessed by treating a biological sample containing proteins with thetest compound. Proteins from the biological sample are incubated withantibodies specific to the polypeptides of the present invention. Theamount of protein recognized by the antibodies is quantified. The amountof protein in the treated biological sample is compared with the amountin an untreated biological sample. A difference in the amount of proteinbetween the two samples is indicative of a toxic response to the testcompound in the treated sample.

[0307] Microarrays may be prepared, used, and analyzed using methodsknown in the art (Brennan, T. M. et al. (1995) U.S. Pat. No. 5,474,796;Schena, M. et al. (1996) Proc. Natl. Acad. Sci. USA 93:10614-10619;Baldeschweileret al. (1995) PCT application WO95/251116; Shalon, D. etal. (1995) PCT application WO95/35505; Heller, R. A. et al. (1997) Proc.Natl. Acad. Sci. USA 94:2150-2155; Heller, M. J. et al. (1997) U.S. Pat.No. 5,605,662). Various types of microarrays are well known andthoroughly described in Schena, M., ed. (1999; DNA Microarrays: APractical Approach, Oxford University Press, London).

[0308] In another embodiment of the invention, nucleic acid sequencesencoding VAP may be used to generate hybridization probes useful inmapping the naturally occurring genomic sequence. Either coding ornoncoding sequences may be used, and in some instances, noncodingsequences may be preferable over coding sequences. For example,conservation of a coding sequence among members of a multi-gene familymay potentially cause undesired cross hybridization during chromosomalmapping. The sequences may be mapped to a particular chromosome, to, aspecific region of a chromosome, or to artificial chromosomeconstructions, e.g., human artificial chromosomes (HACs), yeastartificial chromosomes (YACs), bacterial artificial chromosomes (BACs),bacterial P1 constructions, or single chromosome cDNA libraries(Harrington, J. J. et al. (1997) Nat. Genet. 15:345-355; Price, C. M.(1993) Blood Rev. 7:127-134; Trask, B. J. (1991) Trends Genet.7:149-154). Once mapped, the nucleic acid sequences may be used todevelop genetic linkage maps, for example, which correlate theinheritance of a disease state with the inheritance of a particularchromosome region or restriction fragment length polymorphism (RFLP)(Lander, E. S. and D. Botstein (1986) Proc. Natl. Acad. Sci. USA83:7353-7357).

[0309] Fluorescent in situ hybridization (FISH) may be correlated withother physical and genetic map data (Heinz-Ulrich, et al. (1995) inMeyers, supra, pp. 965-968). Examples of genetic map data can be foundin various scientific journals or at the Online Mendelian Inheritance inMan (OMIM) World Wide Web site. Correlation between the location of thegene encoding VAP on a physical map and a specific disorder, or apredisposition to a specific disorder, may help define the region of DNAassociated with that disorder and thus may further positional cloningefforts.

[0310] In situ hybridization of chromosomal preparations and physicalmapping techniques, such as linkage analysis using establishedchromosomal markers, may be used for extending genetic maps. Often theplacement of a gene on the chromosome of another mammalian species, suchas mouse, may reveal associated markers even if the exact chromosomallocus is not known. This information is valuable to investigatorssearching for disease genes using positional cloning or other genediscovery techniques. Once the gene or genes responsible for a diseaseor syndrome have been crudely localized by genetic linkage to aparticular genomic region, e.g., ataxia-telangiectasia to 1 lq22-23, anysequences mapping to that area may represent associated or regulatorygenes for further investigation (Gatti, R. A. et al. (1988) Nature336:577-580). The nucleotide sequence of the instant invention may alsobe used to detect differences in the chromosomal location due totranslocation, inversion, etc., among normal, carrier, or affectedindividuals.

[0311] In another embodiment of the invention, VAP, its catalytic orimmunogenic fragments, or oligopeptides thereof can be used forscreening libraries of compounds in any of a variety of drug screeningtechniques. The fragment employed in such screening may be free insolution, affixed to a solid support, borne on a cell surface, orlocated intracellularly. The formation of binding complexes between VAPand the agent being tested may be measured.

[0312] Another technique for drug screening provides for high throughputscreening of compounds having suitable binding affinity to the proteinof interest (Geysen, et al. (1984) PCT application WO84/03564). In thismethod, large numbers of different small test compounds are synthesizedon a solid substrate. The test compounds are reacted with VAP, orfragments thereof, and washed. Bound VAP is then detected by methodswell known in the art. Purified VAP can also be coated directly ontoplates for use in the aforementioned drug screening techniques.Alternatively, non-neutralizing antibodies can be used to capture thepeptide and immobilize it on a solid support.

[0313] In another embodiment, one may use competitive drug screeningassays in which neutralizing antibodies capable of binding VAPspecifically compete with a test compound for binding VAP. In thismanner, antibodies can be used to detect the presence of any peptidewhich shares one or more antigenic determinants with VAP.

[0314] In additional embodiments, the nucleotide sequences which encodeVAP may be used in any molecular biology techniques that have yet to bedeveloped, provided the new techniques rely on properties of nucleotidesequences that are currently known, including, but not limited to, suchproperties as the triplet genetic code and specific base pairinteractions.

[0315] Without further elaboration, it is believed that one skilled inthe art can, using the preceding description, utilize the presentinvention to its fullest extent. Thefollowing embodiments are,therefore, to be construed as merely illustrative, and not limitative ofthe remainder of the disclosure in any way whatsoever.

[0316] The disclosures of all patents, applications, and publicationsmentioned above and below, including U.S. Ser. No. 60/347,927, U.S. Ser.No. 60/332,908, U.S. Ser. No. 60/331,865, U.S. Ser. No. 60/342,604, andU.S. Ser. No. 60/354,827, are hereby expressly incorporated byreference.

EXAMPLES

[0317] I. Construction of cDNA Libraries

[0318] Incyte cDNAs were derived from cDNA libraries described in theLIFESEQ GOLD database (Incyte Genomics, Palo Alto Calif.). Some tissueswere homogenized and lysed in guanidinium isothiocyanate, while otherswere homogenized and lysed in phenol or in a suitable mixture ofdenaturants, such as TRIZOL (Invitrogen), a monophasic solution ofphenol and guanidine isothiocyanate. The resulting lysates werecentrifuged over CsCl cushions or extracted with chloroform. RNA wasprecipitated from the lysates with either isopropanol or sodium acetateand ethanol, or by other routine methods.

[0319] Phenol extraction and precipitation of RNA were repeated asnecessary to increase RNA purity. In some cases, RNA was treated withDNase. For most libraries, poly(A)+ RNA was isolated using oligod(T)-coupled paramagnetic particles (Promega), OLIGOTEX latex particles(QIAGEN, Chatsworth Calif.), or an OLIGOTEX mRNA purification kit(QIAGEN). Alternatively, RNA was isolated directly from tissue lysatesusing other RNA isolation kits, e.g., the POLY(A)PURE mRNA purificationkit (Ambion, Austin Tex.).

[0320] In some cases, Stratagene was provided with RNA and constructedthe corresponding cDNA libraries. Otherwise, cDNA was synthesized andcDNA libraries were constructed with the UNIZAP vector system(Stratagene) or SUPERSCRIPT plasmid system (Invitrogen), using therecommended procedures or similar methods known in the art (Ausubel etal., supra, ch. 5). Reverse transcription was initiated using oligo d(T)or random primers. Synthetic oligonucleotide adapters were ligated todouble stranded cDNA, and the cDNA was digested with the appropriaterestriction enzyme or enzymes. For most libraries, the cDNA wassize-selected (300-1000 bp) using SEPHACRYL S1000, SEPHAROSE CL2B, orSEPHAROSE CL4B column chromatography (Amersham Biosciences) orpreparative agarose gel electrophoresis. cDNAs were ligated intocompatible restriction enzyme sites of the polylinker of a suitableplasmid, e.g., PBLUESCRIPT plasmid (Stratagene), PSPORT1 plasmid(Invitrogen, Carlsbad Calif.), PCDNA2.1 plasmid (Invitrogen), PBK-CMVplasmid (Stratagene), PCR2-TOPOTA plasmid (Invitrogen), PCMV-ICISplasmid (Stratagene), pIGEN (Incyte Genomics, Palo Alto Calif.), pRARE(Incyte Genomics), or pINCY (Incyte Genomics), or derivatives thereof.Recombinant plasmids were transformed into competent E. coli cellsincluding XL1-Blue, XL1-BlueMRF, or SOLR from Stratagene or DH5α, DH10B,or ElectroMAX DH10B from Invitrogen.

[0321] II. Isolation of cDNA Clones

[0322] Plasmids obtained as described in Example I were recovered fromhost cells by in vivo excision using the UNIAP vector system(Stratagene) or by cell lysis. Plasmids were purified using at least oneof the following: a Magic or WIARD Minipreps DNA purification system(Promega); an AGTC Miniprep purification kit (Edge Biosystems,Gaithersburg Md.); and QIAWELL 8 Plasmid, QIAWELL 8 Plus Plasmnid,QIAWELL 8 Ultra Plasmid purification systems or the R.E.A.L. PREP 96plasmid purification kit from QIAGEN. Following precipitation, plasmidswere resuspended in 0.1 ml of distilled water and stored, with orwithout lyophilization, at 4° C.

[0323] Alternatively, plasmid DNA was amplified from host cell lysatesusing direct link PCR in a high-throughput format (Rao, V. B. (1994)Anal. Biochem. 216:1-14). Host cell lysis and thermal cycling steps werecarried out in a single reaction mixture. Samples were processed andstored in 84-well plates, and the concentration of amplified plasmid DNAwas quantified fluorometrically sing PICOGREEN dye (Molecular Probes,Eugene Oreg.) and a FLUOROSKAN II fluorescence scanner (Labsystems Oy,Helsinki, Finland).

[0324] III. Sequencing and Analysis

[0325] Incyte cDNA recovered in plasmids as described in Example II weresequenced as follows. Sequencing reactions were processed using standardmethods or high-throughput instrumentation such as the ABI CATALYST 800(Applied Biosystems) thermal cycler or the PTC-200 thermal cycler (MJResearch) in conjunction with the HYDRA microdispenser (RobbinsScientific) or the MICROLAB 2200 (Hamilton) liquid transfer system. cDNAsequencing reactions were prepared using reagents provided by AmershamBiosciences or supplied in ABI sequencing kits such as the ABI PRISMBIGDYE Terminator cycle sequencing ready reaction kit (AppliedBiosystems). Electrophoretic separation of cDNA sequencing reactions anddetection of labeled polynucleotides were carried out using the MEGABACE1000 DNA sequencing system (Amersham Biosciences); the ABI PRISM 373 or377 sequencing system (Applied Biosystems) in conjunction with standardABI protocols and base calling software; or other sequence analysissystems known in the art. Reading frames within the cDNA sequences wereidentified using standard methods (Ausubel et al., supra, ch.

[0326] 7). Some of the cDNA sequences were selected for extension usingthe techniques disclosed in Example VIII.

[0327] The polynucleotide sequences derived from Incyte cDNAs werevalidated by removing vector, linker, and poly(A) sequences and bymasking ambiguous bases, using algorithms and programs based on BLAST,dynamic progranmning, and dinucleotide nearest neighbor analysis. TheIncyte cDNA sequences or translations thereof were then queried againsta selection of public databases such as the GenBank primate, rodent,mammalian, vertebrate, and eukaryote databases, and BLOCKS, PRINTS,DOMO, PRODOM; PROTEOME databases with sequences from Homo sapiens,Rattus norvegicus, Mus musculus, Caenorhabditis elegans, Saccharomycescerevisiae, Schizosaccharomyces pombe, and Candida albicans (IncyteGenomics, Palo Alto Calif.); hidden Markov model (HMM)-based proteinfamily databases such as PFAM, INCY, and TIGRFAM (Haft, D. H. et al.(2001) Nucleic Acids Res. 29:4143); and HMM-based protein domaindatabases such as SMART (Schultz, J. et al. (1998) Proc. Natl. Acad.Sci. USA 95:5857-5864; Letunic, I. et al. (2002) Nucleic Acids Res.30:242-244). (HI is a probabilistic approach which analyzes consensusprimary structures of gene families; see, for example, Eddy, S. R.(1996) Curr. Opin. Struct. Biol. 6:361-365.) The queries were performedusing programs based on BLAST, FASTA, BLIMPS, and HMMER. The Incyte cDNAsequences were assembled to produce full length polynucleotidesequences. Alternatively, GenBank cDNAs, GenBank ESTs, stitchedsequences, stretched sequences, or Genscan-predicted coding sequences(see Examples IV and V) were used to extend Incyte cDNA assemblages tofull length. Assembly was performed using programs based on Phred,Phrap, and Consed, and cDNA assemblages were screened for open readingframes using programs based on GeneMark, BLAST, and FASTA. The fulllength polynucleotide sequences were translated to derive thecorresponding full length polypeptide sequences. Alternatively, apolypeptide may begin at any of the methionine residues of the fulllength translated polypeptide. Full length polypeptide sequences weresubsequently analyzed by querying against databases such as the GenBankprotein databases (genpept), SwissProt, the PROTEOME databases, BLOCKS,PRINTS, DOMO, PRODOM, Prosite, hidden Markov model (HMM)-based proteinfamily databases such as PFAM, INCY, and TIGRFAM; and HMM-based proteindomain databases such as SMART. Full length polynucleotide sequences arealso analyzed using MACDNASIS PRO software (MiraiBio, Alameda Calif.)and LASERGENE software (DNASTAR). Polynucleotide and polypeptidesequence alignments are generated using default parameters specified bythe CLUSTAL algorithm as incorporated into the MBGALIGN multisequencealignment program (DNASTAR), which also calculates the percent identitybetween aligned sequences.

[0328] Table 7 summarizes the tools, programs, and algorithms used forthe analysis and assembly of Incyte cDNA and full length sequences andprovides applicable descriptions, references, and threshold parameters.The first column of Table 7 shows the tools, programs, and algorithmsused, the second column provides brief descriptions thereof, the thirdcolumn presents appropriate references, all of which are incorporated byreference herein in their entirety, and the fourth column presents,where applicable, the scores, probability values, and other parametersused to evaluate the strength of a match between two sequences (thehigher the score or the lower the probability value, the greater theidentity between two sequences).

[0329] The programs described above for the assembly and analysis offull length polynucleotide and polypeptide sequences were also used toidentify polynucleotide sequence fragments from SEQ ID NO:21-40.Fragments from about 20 to about 4000 nucleotides which are useful inhybridization and amplification technologies are described in Table 4,column 2.

[0330] IV. Identification and Editing of Coding Sequences from GenomicDNA

[0331] Putative vesicle-associated proteins were initially identified byrunning the Genscan gene identification program against public genomicsequence databases (e.g., gbpri and gbhtg). Genscan is a general-purposegene identification program which analyzes genomic DNA sequences from avariety of organisms (Burge, C. and S. Karlin (1997) J. Mol. Biol.268:78-94; Burge, C. and S. Karlin (1998) Curr. Opin. Struct. Biol.8:346-354). The program concatenates predicted exons to form anassembled cDNA sequence extending from a methionine to a stop codon. Theoutput of Genscan is a FASTA database of polynucleotide and polypeptidesequences. The maximum range of sequence for enscan to analyze at oncewas set to 30 kb. To determine which of these Genscan predicted cDNAequences encode vesicle-associated proteins, the encoded polypeptideswere analyzed by querying against PFAM models for vesicle-associatedproteins. Potential vesicle-associated proteins were also identified byhomology to Incyte cDNA sequences that had been annotated asvesicle-associated proteins. These selected Genscan-predicted sequenceswere then compared by BLAST analysis to the genpept and gbpri publicdatabases. Where necessary, the Genscan-predicted sequences were thenedited by comparison to the top BLAST hit from genpept to correct errorsin the sequence predicted by Genscan, such as extra or omitted exons.BLAST analysis was also used to find any Incyte cDNA or public cDNAcoverage of the Genscan-predicted sequences, thus providing evidence fortranscription. When Incyte cDNA coverage was available, this informationwas used to correct or confirm the Genscan predicted sequence. Fulllength polynucleotide sequences were obtained by assemblingGenscan-predicted coding sequences with Incyte cDNA sequences and/orpublic cDNA sequences using the assembly process described in ExampleIII. Alternatively, full length polynucleotide sequences were derivedentirely from edited or unedited Genscan-predicted coding sequences.

[0332] V. Assembly of Genomnic Sequence Data with cDNA Sequence Data“Stitched” Sequences

[0333] Partial cDNA sequences were extended with exons predicted by theGenscan gene identification program described in Example IV. PartialcDNAs assembled as described in Example m were mapped to genomic DNA andparsed into clusters containing related cDNAs and Genscan exonpredictions from one or more genomic sequences. Each cluster wasanalyzed using an algorithm based on graph theory and dynamicprogramming to integrate cDNA and genomic information, generatingpossible splice variants that were subsequently confirmed, edited, orextended to create a full length sequence. Sequence intervals in whichthe entire length of the interval was present on more than one sequencein the cluster were identified, and intervals thus identified wereconsidered to be equivalent by transitivity. For example, if an intervalwas present on a cDNA and two genomic sequences, then all threeintervals were considered to be equivalent. This process allowsunrelated but consecutive genomic sequences to be brought together,bridged by cDNA sequence. Intervals thus identified were then “stitched”together by the stitching algorithm in the order that they appear alongtheir parent sequences to generate the longest possible sequence, aswell as sequence variants. Linkages between intervals which proceedalong one type of parent sequence (cDNA to cDNA or genomic sequence togenomic sequence) were given preference over linkages which changeparent type (cDNA to genomic sequence). The resultant stitched sequenceswere translated and compared by BLAST analysis to the genpept and gbpripublic databases. Incorrect exons predicted by Genscan were corrected bycomparison to the top BLAST hit from genpept. Sequences were furtherextended with additional cDNA sequences, or by inspection of genomicDNA, when necessary.

[0334] “Stretched” Sequences

[0335] Partial DNA sequences were extended to full length with analgorithm based on BLAST analysis. First, partial cDNAs assembled asdescribed in Example m were queried against public databases such as theGenBank primate, rodent, mammalian, vertebrate, and eukaryote databasesusing the BLAST program. The nearest GenBank protein homolog was thencompared by BLAST analysis to either Incyte cDNA sequences or GenScanexon predicted sequences described in Example IV. A chimeric protein wasgenerated by using the resultant high-scoring segment pairs (HSPs) tomap the translated sequences onto the GenBank protein homolog.Insertions or deletions may occur in the chimeric protein with respectto the original GenBank protein homolog. The GenBank protein homolog,the chimeric protein, or both were used as probes to search forhomologous genomic sequences from the public human genome databases.Partial DNA sequences were therefore “stretched” or extended by theaddition of homologous genomic sequences. The resultant stretchedsequences were examined to determine whether it contained a completegene.

[0336] VI. Chromosomal Mapping of VAP Encoding Polynucleotides

[0337] The sequences which were used to assemble SEQ ID NO:21-40 werecompared with sequences from the Incyte LIFESEQ database and publicdomain databases using BLAST and other implementations of theSmith-Waterman algorithm. Sequences from these databases that matchedSEQ ID NO:21-40 were assembled into clusters of contiguous andoverlapping sequences using assembly algorithms such as Phrap (Table 7).Radiation hybrid and genetic mapping data available from publicresources such as the Stanford Human Genome Center (SHGC), WhiteheadInstitute for Genome Research (WIGR), and Généthon were used todetermine if any of the clustered sequences had been previously mapped.Inclusion of a mapped sequence in a cluster resulted in the assignmentof all sequences of that cluster, including its particular SEQ ID NO:,to that map location.

[0338] Map locations are represented by ranges, or intervals, of humanchromosomes. The map position of an interval, in centiMorgans, ismeasured relative to the terminus of the chromosome's p-arm. (Thecentimorgan (cM) is a unit of measurement based on recombinationfrequencies between chromosomal markers. On average, 1 cM is roughlyequivalent to 1 megabase (Mb) of DNA in humans, although this can varywidely due to hot and cold spots of recombination.) The cM distances arebased on genetic markers mapped by Généthon which provide boundaries forradiation hybrid markers whose sequences were included in each of theclusters. Human genome maps and other resources available to the public,such as the NCBI “GeneMap'99” World Wide Web site(http://www.ncbi.nlm.nih.gov/genemap/), can be employed to determine ifpreviously identified disease genes map within or in proximity to theintervals indicated above.

[0339] VII. Analysis of Polynucleotide Expression

[0340] Northern analysis is a laboratory technique used to detect thepresence of a transcript of a gene and involves the hybridization of alabeled nucleotide sequence to a membrane on which RNAs from aparticular cell type or tissue have been bound (Sambrook and Russell,supra, ch. 7; Ausubel et al., supra, ch. 4).

[0341] Analogous computer techniques applying BLAST were used to searchfor identical or related molecules in databases such as GenBank orLIFESEQ (Incyte Genomics). This analysis is much faster than multiplemembrane-based hybridizations. In addition, the sensitivity of thecomputer search can be modified to determine whether any particularmatch is categorized as exact or similar. The basis of the search is theproduct score, which is defined as:$\frac{{BLAST}\quad {Score} \times {Percent}\quad {Identity}}{5 \times {minimum}\left\{ {{{length}\left( {{Seq}.\quad 1} \right)},{{length}\left( {{Seq}.\quad 2} \right)}} \right\}}$

[0342] The product score takes into account both the degree ofsimilarity between two sequences and the length of the sequence match.The product score is a normalized value between 0 and 100, and iscalculated as follows: the BLAST score is multiplied by the percentnucleotide identity and the product is divided by (5 times the length ofthe shorter of the two sequences). The BLAST score is calculated byassigning a score of +5 for every base that matches in a high-scoringsegment pair (HSP), and 4 for every mismatch. Two sequences may sharemore than one HSP (separated by gaps). If there is more than one HSP,then the pair with the highest BLAST score is used to calculate theproduct score. The product score represents a balance between fractionaloverlap and quality in a BLAST alignment. For example, a product scoreof 100 is produced only for 100% identity over the entire length of theshorter of the two sequences being compared. A product score of 70 isproduced either by 100% identity and 70% overlap at one end, or by 88%identity and 100% overlap at the other. A product score of 50 isproduced either by 100% identity and 50% overlap at one end, or 79%identity and 100% overlap.

[0343] Alternatively, polynucleotides encoding VAP are analyzed withrespect to the tissue sources from which they were derived. For example,some full length sequences are assembled, at least in part, withoverlapping Incyte cDNA sequences (see Example E). Each cDNA sequence isderived from a cDNA library constructed from a human tissue. Each humantissue is classified into one of the following organ/tissue categories:cardiovascular system; connective tissue; digestive system; embryonicstructures; endocrine system; exocrine glands; genitalia, female;genitalia, male; germ cells; hemic and immune system; liver;musculoskeletal system; nervous system; pancreas; respiratory system;sense organs; skin; stomatognathic system; unclassified/mixed; orurinary tract. The number of libraries in each category is counted anddivided by the total number of libraries across all categories.Similarly, each human tissue is classified into one of the followingdisease/condition categories: cancer, cell line, developmental,inflammation, neurological, trauma, cardiovascular, pooled, and other,and the number of libraries in each category is counted and divided bythe total number of libraries across all categories. The resultingpercentages reflect the tissue- and disease-specific expression of cDNAencoding VAP. cDNA sequences and cDNA library/tissue information arefound in the LIFESEQ GOLD database (Incyte Genomics, Palo Alto Calif.).

[0344] VIII. Extension of VAP Encoding Polynucleotides

[0345] Full length polynucleotides are produced by extension of anappropriate fragment of the full. length molecule using oligonucleotideprimers designed from this fragment. One primer was synthesized toinitiate 5′ extension of the known fragment, and the other primer wassynthesized to initiate 3′ extension of the known fragment. The initialprimers were designed using OLIGO 4.06 software (National Biosciences),or another appropriate program, to be about 22 to 30 nucleotides inlength, to have a GC content of about 50% or more, and to anneal to thetarget sequence at temperatures of about 68° C. to about 72° C. Anystretch of nucleotides which would result in hairpin structures andprimer-primer dimerizations was avoided.

[0346] Selected human cDNA libraries were used to extend the sequence.If more than one extension was necessary or desired, additional ornested sets of primers were designed.

[0347] High fidelity amplification was obtained by PCR using methodswell known in the art. PCR was performed in 96-well plates using thePTC-200 thermal cycler (MJ Research, Inc.). The reaction mix containedDNA template, 200 nmol of each primer, reaction buffer containing Me²⁺,(NH₄)₂SO₄, and 2-mercaptoethanol, Taq DNA polymerase (AmershamBiosciences), ELONGASE enzyme (Invitrogen), and Pfu DNA polymerase(Stratagene), with the following parameters for primer pair PCI A andPCI B: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 60° C., 1min; Step 4: 68° C., 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times;Step 6: 68° C., 5 min; Step 7: storage at 4° C. In the alternative, theparameters for primer pair T7 and SK+ were as follows: Step 1: 94° C., 3min; Step 2: 94° C., 15 sec; Step 3: 57° C., 1 min; Step 4: 68° C., 2min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68° C., 5 min;Step 7: storage at 4° C.

[0348] The concentration of DNA in each well was determined bydispensing 100 μl PICOGREEN quantitation reagent (0.25% (v/v) PICOGREEN;Molecular Probes, Eugene Oreg.) dissolved in 1×TE and 0.5 μl ofundiluted PCR product into each well of an opaque fluorimeter plate(Corning Costar, Acton Mass.), allowing the DNA to bind to the reagent.The plate was scanned in a Fluoroskan II (Labsystems Oy, Helsinki,Finland) to measure the fluorescence of the sample and to quantify theconcentration of DNA. A 5 μl to 10 μl aliquot of the reaction mixturewas analyzed by electrophoresis on a 1% agarose gel to determine whichreactions were successful in extending the sequence.

[0349] The extended nucleotides were desalted and concentrated,transferred to 384-well plates, digested with CviJI cholera virusendonuclease (Molecular Biology Research, Madison Wis.), and sonicatedor sheared prior to religation into pUC 18 vector (AmershamBiosciences). For shotgun sequencing, the digested nucleotides wereseparated on low concentration (0.6 to 0.8%) agarose gels, fragmentswere excised, and agar digested with Agar ACE (Promega). Extended cloneswere religated using T4 ligase (New England Biolabs, Beverly Mass.) intopUC 18 vector (Amersham Biosciences), treated with Pfu DNA polymerase(Stratagene) to fill-in restriction site overhangs, and transfected intocompetent E. coli cells. Transformed cells were selected onantibiotic-containing media, and individual colonies were picked andcultured overnight at 37° C. in 384-well plates in LB/2×carb liquidmedia.

[0350] The cells were lysed, and DNA was amplified by PCR using Taq DNApolymerase (Amersham Biosciences) and Pfu DNA polymerase (Stratagene)with the following parameters: Step 1: 94° C., 3 min; Step 2: 94° C., 15sec; Step 3: 60° C., 1 min; Step 4: 72° C., 2 min; Step 5: steps 2, 3,and 4 repeated 29 times; Step 6: 72° C., 5 min; Step 7: storage at 4° C.DNA was quantified by PICOGREEN reagent (Molecular Probes) as describedabove. Samples with low DNA recoveries were reamplified using the sameconditions as described above. Samples were diluted with 20%dimethysulfoxide (1:2, v/v), and sequenced using DYENAMIC energytransfer sequencing primers and the DYENAMIC DIRECT kit (AmershamBiosciences) or the ABI PRISM BIGDYE Terminator cycle sequencing readyreaction kit (Applied Biosystems).

[0351] In like manner, full length polynucleotides are verified usingthe above procedure or are used to obtain 5′ regulatory sequences usingthe above procedure along with oligonucleotides designed for suchextension, and an appropriate genomic library.

[0352] IX. Identification of Single Nucleotide Polymorphisms in VAPEncoding Polynucleotides

[0353] Common DNA sequence variants known as single nucleotidepolymorphisms (SNPs) were identified in SEQ ID NO:21-40 using theLIFESEQ database (Incyte Genomics). Sequences from the same gene wereclustered together and assembled as described in Example m, allowing theidentification of all sequence variants in the gene. An algorithmconsisting of a series of filters was used to distinguish SNPs fromother sequence variants. Preliminary filters removed the majority ofbasecall errors by requiring a minimum Phred quality score of 15, andremoved sequence alignment errors and errors resulting from impropertrimming of vector sequences, chimeras, and splice variants. Anautomated procedure of advanced chromosome analysis analysed theoriginal chromatogram files in the vicinity of the putative SNP. Cloneerror filters used statistically generated algorithms to identify errorsintroduced during laboratory processing, such as those caused by reversetranscriptase, polymerase, or somatic mutation. Clustering error filtersused statistically generated algorithms to identify errors resultingfrom clustering of close homologs or pseudogenes, or due tocontamination by non-human sequences. A final set of filters removedduplicates and SNPs found in immunoglobulins or T-cell receptors.

[0354] Certain SNPs were selected for further characterization by massspectrometry using the high throughput MASSARRAY system (Sequenom, Inc.)to analyze allele frequencies at the SNP sites in four different humanpopulations. The Caucasian population comprised 92 individuals (46 male,46 female), including 83 from Utah, four French, three Venezualan, andtwo Amish individuals. The African population comprised 194 individuals(97 male, 97 female), all African Americans. The Hispanic populationcomprised 324 individuals (162 male, 162 female), all Mexican Hispanic.The Asian population comprised 126 individuals (64 male, 62 female) witha reported parental breakdown of 43% Chinese, 31% Japanese, 13% Korean,5% Vietnamese, and 8% other Asian. Allele frequencies were firstanalyzed in the Caucasian population; in some cases those SNPs whichshowed no allelic variance in this population were not further tested inthe other three populations.

[0355] X. Labeling and Use of Individual Hybridization Probes

[0356] Hybridization probes derived from SEQ ID NO:21-40 are employed toscreen cDNAs, genomic DNAs, or mRNAs. Although the labeling ofoligonucleotides, consisting of about 20 base pairs, is specificallydescribed, essentially the same procedure is used with larger nucleotidefragments. Oligonucleotides are designed using state-of-the-art softwaresuch as OLIGO 4.06 software (National Biosciences) and labeled bycombining 50 pmol of each oligomer, 250 μCi of [γ-³²P] adenosinetriphosphate (Amersham Biosciences), and T4 polynucleotide kinase(DuPont NEN, Boston Mass.). The labeled oligonucleotides aresubstantially purified using a SEPHADEX G-25 superfine size exclusiondextran bead column (Amersham Biosciences). An aliquot containing 107counts per minute of the labeled probe is used in a typicalmembrane-based hybridization analysis of human genomic DNA digested withone of the following endonucleases: Ase I, Bgl II, Eco RI, Pst I, Xba I,or Pvu II (DuPont NEN).

[0357] The DNA from each digest is fractionated on a 0.7% agarose geland transferred to nylon membranes (Nytran Plus, Schleicher & Schuell,Durham N.H.). Hybridization is carried out for 16 hours at 40° C. Toremove nonspecific signals, blots are sequentially washed at roomtemperature under conditions of up to, for example, 0.1×saline sodiumcitrate and 0.5% sodium dodecyl sulfate. Hybridization patterns arevisualized using autoradiography or an alternative imaging means andcompared.

[0358] XI. Microarrays

[0359] The linkage or synthesis of array elements upon a microarray canbe achieved utilizing photolithography, piezoelectric printing (inkjetprinting; see, e.g., Baldeschweiler et al., supra), mechanicalmicrospotting technologies, and derivatives thereof. The substrate ineach of the aforementioned technologies should be uniform and solid witha non-porous surface (Schena, M., ed. (1999) DNA Microarrays: APractical Approach, Oxford University Press, London). Suggestedsubstrates include silicon, silica, glass slides, glass chips, andsilicon wafers. Alternatively, a procedure analogous to a dot or slotblot may also be used to arrange and link elements to the surface of asubstrate using thermal, UV, chemical, or mechanical bonding procedures.A typical array may be produced using available methods and machineswell known to those of ordinary skill in the art and may contain anyappropriate number of elements (Schena, M. et al. (1995) Science270:467-470; Shalon, D. et al. (1996) Genome Res. 6:639-645; Marshall,A. and J. Hodgson (1998) Nat. Biotechnol. 16:27-31).

[0360] Full length cDNAs, Expressed Sequence Tags (ESTs), or fragmentsor oligomers thereof may comprise the elements of the microarray.Fragments or oligomers suitable for hybridization can be selected usingsoftware well known in the art such as LASERGENE software (DNASTAR). Thearray elements are hybridized with polynucleotides in a biologicalsample. The polynucleotides in the biological sample are conjugated to afluorescent label or other molecular tag for ease of detection. Afterhybridization, nonhybridized nucleotides from the biological sample areremoved, and a fluorescence scanner is used to detect hybridization ateach array element. Alternatively, laser desorbtion and massspectrometry may be used for detection of hybridization. The degree ofcomplementarity and the relative abundance of each polynucleotide whichhybridizes to an element on the microarray may be assessed. In oneembodiment, microarray preparation and usage is described in detailbelow.

[0361] Tissue or Cell Sample Preparation

[0362] Total RNA is isolated from tissue samples using the guanidiniumthiocyanate method and poly(A)⁺ RNA is purified using the oligo-(dT)cellulose method. Each poly(A)⁺ RNA sample is reverse transcribed usingMMLV reverse-transcriptase, 0.05 μg/μl oligo-(dT) primer (21 mer),1×first strand buffer, 0.03 units/μl RNase inhibitor, 500 μM DATP, 500μM dGTP, 500 μM dTTP, 40 μM dCTP, 40 μM dCTP-Cy3 (BDS) or dCTP-CyS(Amersham Biosciences). The reverse transcription reaction is performedin a 25 ml volume containing 200 ng poly(A)⁺ RNA with GEMBRIGHT kits(Incyte Genomics). Specific control poly(A)⁺ RNAs are synthesized by invitro transcription from non-coding yeast genomic DNA. After incubationat 37° C. for 2 hr, each reaction sample (one with Cy3 and another withCy5 labeling) is treated with 2.5 ml of 0.5M sodium hydroxide andincubated for 20 minutes at 85° C. to the stop the reaction and degradethe RNA. Samples are purified using two successive CHROMA SPIN 30 gelfiltration spin columns (Clontech, Palo Alto Calif.) and aftercombining, both reaction samples are ethanol precipitated using 1 ml ofglycogen (1 mg/ml), 60 ml sodium acetate, and 300 ml of 100% ethanol.The sample is then dried to completion using a SpeedVAC (SavantInstruments Inc., Holbrook N.Y.) and resuspended in 14 μl 5×SSC/0.2%SDS.

[0363] Microarray Preparation

[0364] Sequences of the present invention are used to generate arrayelements. Each array element is amplified from bacterial cellscontaining vectors with cloned cDNA inserts. PCR amplification usesprimers complementary to the vector sequences flanking the cDNA insert.Array elements are amplified in thirty cycles of PCR from an initialquantity of 1-2 ng to a final quantity greater than 5 μg. Amplifiedarray elements are then purified using SEPHACRYL-400 (AmershamBiosciences).

[0365] Purified array elements are immobilized on polymer-coated glassslides. Glass microscope slides (Corning) are cleaned by ultrasound in0.1% SDS and acetone, with extensive distilled water washes between andafter treatments. Glass slides are etched in 4% hydrofluoric acid (VWRScientific Products Corporation (VWR), West Chester Pa.), washedextensively in distilled water, and coated with 0.05% aminopropyl silane(Sigma) in 95% ethanol. Coated slides are cured in a 110° C. oven.

[0366] Array elements are applied to the coated glass substrate using aprocedure described in U.S. Pat. No. 5,807,522, incorporated herein byreference. 1 μl of the array element DNA, at an average concentration of100 ng/μl, is loaded into the open capillary printing element by ahigh-speed robotic apparatus. The apparatus then deposits about 5 nl ofarray element sample per slide.

[0367] Microarrays are UV-crosslinked using a STRATALINKERUV-crosslinker (Stratagene). Microarrays are washed at room temperatureonce in 0.2% SDS and three times in distilled water. Non-specificbinding sites are blocked by incubation of microarrays in 0.2% casein inphosphate buffered saline (PBS) (Tropix, Inc., Bedford Mass.) for 30minutes at 60° C. followed by washes in 0.2% SDS and distilled water asbefore.

[0368] Hybridization

[0369] Hybridization reactions contain 9 μl of sample mixture consistingof 0.2 μg each of Cy3 and Cy5 labeled cDNA synthesis products in 5×SSC,0.2% SDS hybridization buffer. The sample mixture is heated to 65° C.for 5 minutes and is aliquoted onto the microarray surface and coveredwith an 1.8 cm² coverslip. The arrays are transferred to a waterproofchamber having a cavity just slightly larger than a microscope slide.The chamber is kept at 100% humidity internally by the addition of 140μl of 5×SSC in a corner of the chamber. The chamber containing thearrays is incubated for about 6.5 hours at 60° C. The arrays are washedfor 10 min at 45° C. in a first wash buffer (1×SSC, 0.1% SDS), threetimes for 10 minutes each at 45° C. in a second wash buffer (0.1×SSC),and dried.

[0370] Detection

[0371] Reporter-labeled hybridization complexes are detected with amicroscope equipped with an Innova 70 mixed gas 10 W laser (Coherent,Inc., Santa Clara Calif.) capable of generating spectral lines at 488 nmfor excitation of Cy3 and at 632 nm for excitation of CyS. Theexcitation laser light is focused on the array using a 20× microscopeobjective (Nikon, Inc., Melville N.Y.). The slide containing the arrayis placed on a computer-controlled X-Y stage on the microscope andraster-scanned past the objective. The 1.8 cm×1.8 cm array used in thepresent example is scanned with a resolution of 20 micrometers.

[0372] In two separate scans, a mixed gas multiline laser excites thetwo fluorophores sequentially. Emitted light is split, based onwavelength, into two photomultiplier tube detectors (PMT R1477,Hamamatsu Photonics Systems, Bridgewater N.J.) corresponding to the twofluorophores. Appropriate filters positioned between the array and thephotomultiplier tubes are used to filter the signals. The emissionmaxima of the fluorophores used are 565 nm for Cy3 and 650 nm for Cy5.Each array is typically scanned twice, one scan per fluorophore usingthe appropriate filters at the laser source, although the apparatus iscapable of recording the spectra from both fluorophores simultaneously.

[0373] The sensitivity of the scans is typically calibrated using thesignal intensity generated by a cDNA control species added to the samplemixture at a known concentration. A specific location on the arraycontains a complementary DNA sequence, allowing the intensity of thesignal at that location to be correlated with a weight ratio ofhybridizing species of 1:100,000. When two samples from differentsources (e.g., representing test and control cells), each labeled with adifferent fluorophore, are hybridized to a single array for the purposeof identifying genes that are differentially expressed, the calibrationis done by labeling samples of the calibrating cDNA with the twofluorophores and adding identical amounts of each to the hybridizationmixture.

[0374] The output of the photomultiplier tube is digitized using a12-bit RTI-835H analog-to-digital (A/D) conversion board (AnalogDevices, Inc., Norwood Mass.) installed in an IBM-compatible PCcomputer. The digitized data are displayed as an image where the signalintensity is mapped using a linear 20-color transformation to apseudocolor scale ranging from blue (low signal) to red (high signal).The data is also analyzed quantitatively. Where two differentfluorophores are excited and measured simultaneously, the data are firstcorrected for optical crosstalk (due to overlapping emission spectra)between the fluorophores using each fluorophore's emission spectrum.

[0375] A grid is superimposed over the fluorescence signal image suchthat the signal from each spot is centered in each element of the grid.The fluorescence signal within each element is then integrated to obtaina numerical value corresponding to the average intensity of the signal.The software used for signal analysis is the GEMTOOLS gene expressionanalysis program (Incyte Genomics). Array elements that exhibit at leastabout a two-fold change in expression, a signal-to-background ratio ofat least about 2.5, and an element spot size of at least about 40%, areconsidered to be differentially expressed.

[0376] Expression

[0377] For example, SEQ ID NO:30 and SEQ ID NO:33 showed differentialexpression in certain breast carcinoma cell lines versus primary mammaryepithelial cells as determined by microarray analysis. The geneexpression profile of a primary mammary epithelial cell line, HMEC, wascompared to the gene expression profiles of breast carcinoma lines atdifferent stages of tumor progression. Cell lines compared included: a)MCF7, a nonmalignant breast adenocarcinoma cell line isolated from thepleural effusion of a 69-year-old female; b) T47D, a breast carcinomacell line isolated from a pleural effusion obtained from a 54-year-oldfemale with an infiltrating ductal carcinoma of the breast; c) Sk-BR-3,a breast adenocarcinoma cell line isolated from a malignant pleuraleffusion of a 43-year-old female; d) BT-20, a breast carcinoma cell linederived int vitro from tumor mass isolated from a 74-year-old female; e)MDA-mb-435S, a spindle shaped strain that evolved from the parent line(435) isolated from the pleural effusion of a 31-year-old female withmetastatic, ductal adenocarcinoma of the breast; and f) MDA-mb-231, ametastatic breast tumor cell line derived from the pleural effusion of a51-year-old female with metastatic breast carcinoma. The microarrayexperiments showed that the expression of SEQ ID NO:30 and SEQ ID NO:33were decreased by at least two fold in cells from carcinoma cell lines(MCF7, Sk-BR-3, and T47D) relative to cells from the primary mammaryepithelial cell line, HMEC. Therefore, in various embodiments, SEQ IDNO:30 and SEQ ID NO:33 can be used for one or more of the following: i)monitoring treatment of breast cancer, ii) diagnostic assays for breastcancer, and iii) developing therapeutics and/or other treatments forbreast cancer.

[0378] Furthermore, the expression of SEQ ID NO:30 and SEQ ID NO:33 weredecreased by at least two-fold in treated human adipocytes from obeseand normal donors when compared to non-treated adipocytes from the samedonors. The normal human primary subcutaneous preadipocytes wereisolated from adipose tissue of a 28-year-old healthy female with a bodymass index (BMI) of 23.59.

[0379] The obese human primary subcutaneous preadipocytes were isolatedfrom adipose tissue of a 40-year-old healthy female with a body massindex (BMI) of 32.47. The preadipocytes were cultured and induced todifferentiate into adipocytes by culturing them in the differentiationmedium containing the active components, PPAR-γ agonist and humaninsulin. Human preadipocytes were treated with human insulin and PPAR-γagonist for three days and subsequently were switched to mediumcontaining insulin for 24 hours, 48 hours, four days, 8 days or 15 daysbefore the cells were collected for analysis. Differentiated adipocyteswere compared to untreated preadipocytes maintained in culture in theabsence of inducing agents. Between 80% and 90% of the preadipocytesfinally differentiated to adipocytes as observed under phase contrastmicroscope. Therefore, in various embodiments, SEQ ID NO:30 and SEQ IDNO:33 can be used for one or more of the following: i) monitoringtreatment of diabetes mellitus and other disorders, such as obesity,hypertension, and atherosclerosis, ii) diagnostic assays for diabetesmellitus and other disorders, such as obesity, hypertension, andatherosclerosis, and iii) developing therapeutics and/or othertreatments for diabetes mellitus and other disorders, such as obesity,hypertension, and atherosclerosis.

[0380] In yet another example, SEQ ID NO:30 showed differentialexpression in the PC3 prostate carcinoma cell line versus normalprostate epithelial cells as determined by microarray analysis. Threeprostate carcinoma cell lines, DU145, LNCAP, and PC-3 were included inthe experiments. DU145 was isolated from a metastatic site in the brainof a 69-year-old male with widespread metastatic prostate carcinoma.DU145 has no detectable sensitivity to hormones; forms colonies insemi-solid medium; is only weekly positive for acid phosphatase; andcells are negative for prostate specific antigen (PSA). LNCaP is aprostate carcinoma cell line isolated from a lymph node biopsy of a50-year-old male with metastatic prostate carcinoma. LNCaP expressesPSA, produces prostate acid phosphatase, and expresses androgenreceptors. PC-3, a prostate adenocarcinoma cell line, was isolated froma metastatic site in the bone of a 62-year-old male with grade IVprostate adenocarcinoma. The normal epithelial cell line, PrEC, is aprimary prostate epithelial cell line isolated from a normal donor. Inone experiment, the expression of cDNAs from the prostate carcinoma celllines representing various stages of prostate tumor progression werecompared with that of the normal prostate epithelial cells under thesame culture conditions. The result from this experiment showed that theexpression of SEQ ID NO:30 was decreased by at least two fold in PC3cells compared to PrEC cells. In a separate experiment, the expressionof cDNAs from the prostate carcinoma cell lines grown under optimalconditions (in the presence of growth factors and nutrients) werecompared to that of the normal prostate epithelial cells grown underrestrictive conditions (in the absence of growth factors and hormones).This experiment showed that the expression of SEQ ID NO:30 was decreasedby at least two fold in PC-3 prostate carcinoma lines grown underoptimal conditions relative to PrECs grown under restrictive conditions.Therefore, in various embodiments, SEQ ID NO:30 can be used for one ormore of the following: i) monitoring treatment of prostate cancer, ii)diagnostic assays for prostate cancer, and iii) developing therapeuticsand/or other treatments for prostate cancer.

[0381] In another example, SEQ ID NO:40 was differentially expressed intreated as compared to untreated human THP-1 cells. THP-1 cells are apromonocyte cell line isolated from the peripheral blood of a 1-year-oldmale with acute monocytic leukemia. Upon stimulation with PMA, THP-1differentiates into macrophage-like cells that display manycharacteristics of peripheral human macrophages. THP-1 cells have beenextensively used in the study of signaling in human monocytes and theidentification of new factors produced by human monocytes. PMA activatoris a broad activator of the protein kinase C-dependent pathways.Ionomycin is a calcium-ionophore that permits the entry of calcium inthe cell, thus increasing the cytosolic calcium concentration. Thecombination of PMA and ionomycin activates two of the major signalingpathways used by mammalian cells to interact with their environment. InT cells, the combination of PMA and ionomycin mimics the type ofsecondary signaling events elicited during optimal B cell activation.

[0382] THP-1 cells were stimulated in vitro with soluble PMA andionomycin for 0.5, 1, 2, 4, and 8 hours. The treated cells were comparedto untreated THP-1 cells kept in culture in the absence of stimuli. SEQID NO:40 was overexpressed by at least two-fold in THP-1 cells treatedfor 2, 4, and 8 hours as compared to untreated counterparts. Therefore,in various embodiments, SEQ ID NO:40 can be used for one or more of thefollowing: i) monitoring treatment of autoimmune/inflammatory disorders,ii) diagnostic assays for autoimmune/inflammatory disorders, and iii)developing therapeutics and/or other treatments forautoimmune/inflammatory disorders.

[0383] XI. Complementary Polynucleotides

[0384] Sequences complementary to the VAP-encoding sequences, or anyparts thereof, are used to detect, decrease, or inhibit expression ofnaturally occurring VAP. Although use of oligonucleotides comprisingfrom about 15 to 30 base pairs is described, essentially the sameprocedure is used with smaller or with larger sequence fragments.Appropriate oligonucleotides are designed using OLIGO 4.06 software(National Biosciences) and the coding sequence of VAP. To inhibittranscription, a complementary oligonucleotide is designed from the mostunique 5′ sequence and used to prevent promoter binding to the codingsequence. To inhibit translation, a complementary oligonucleotide isdesigned to prevent ribosomal binding to the VAP-encoding transcript.

[0385] XIII. Expression of VAP

[0386] Expression and purification of VAP is achieved using bacterial orvirus-based expression systems. For expression of VAP in bacteria, cDNAis subcloned into an appropriate vector containing an antibioticresistance gene and an inducible promoter that directs high levels ofcDNA transcription. Examples of such promoters include, but are notlimited to, the trp-lac (tac) hybrid promoter and the T5 or T7bacteriophage promoter in conjunction with the lac operator regulatoryelement. Recombinant vectors are transformed into suitable bacterialhosts, e.g., BL21(DE3). Antibiotic resistant bacteria express VAP uponinduction with isopropyl beta-D-thiogalactopyranoside (IPTG). Expressionof VAP in eukaryotic cells is achieved by infecting insect or mammaliancell lines with recombinant Autographica californica nuclearpolyhedrosis virus (AcMNPV), commonly known as baculovirus. Thenonessential polyhedrin gene of baculovirus is replaced with cDNAencoding VAP by either homologous recombination or bacterial-mediatedtransposition involving transfer plasmid intermediates. Viralinfectivity is maintained and the strong polyhedrin promoter drives highlevels of cDNA transcription. Recombinant baculovirus is used to infectSpodoptera frugiperda (Sf9) insect cells in most cases, or humanhepatocytes, in some cases. Infection of the latter requires additionalgenetic modifications to baculovirus (Engelhard, E. K. et al. (1994)Proc. Natl. Acad. Sci. USA 91:3224-3227; Sandig, V. et al. (1996) Hum.Gene Ther. 7:1937-1945).

[0387] In most expression systems, VAP is synthesized as a fusionprotein with, e.g., glutathione S-transferase (GST) or a peptide epitopetag, such as FLAG or 6-His, permitting rapid, single-step,affinity-based purification of recombinant fusion protein from crudecell lysates. GST, a 26-kilodalton enzyme from Schistosoma japonicum,enables the purification of fusion proteins on immobilized glutathioneunder conditions that maintain protein activity and antigenicity(Amersham Biosciences). Following purification, the GST moiety can beproteolytically cleaved from VAP at specifically engineered sites. FLAG,an 8-amino acid peptide, enables immunoaffinity purification usingcommercially available monoclonal and polyclonal anti-FLAG antibodies(Eastman Kodak). 6-His, a stretch of six consecutive histidine residues,enables purification on metal-chelate resins (QIAGEN). Methods forprotein expression and purification are discussed in Ausubel et al.(supra, ch. 10 and 16). Purified VAP obtained by these methods can beused directly in the assays shown in Examples XVII and xvm, whereapplicable.

[0388] XIV. Functional Assays

[0389] VAP function is assessed by expressing the sequences encoding VAPat physiologically elevated levels in mammalian cell culture systems.cDNA is subcloned into a mammalian expression vector containing a strongpromoter that drives high levels of cDNA expression. Vectors of choiceinclude PCMV SPORT plasmid (Invitrogen, Carlsbad Calif.) and PCR3.1plasmid (Invitrogen), both of which contain the cytomegaloviruspromoter. 5-10 μg of recombinant vector are transiently transfected intoa human cell line, for example, an endothelial or hematopoietic cellline, using either liposome formulations or electroporation. 1-2 μg ofan additional plasmid containing sequences encoding a marker protein areco-transfected. Expression of a marker protein provides a means todistinguish transfected cells from nontransfected cells and is areliable predictor of cDNA expression from the recombinant vector.Marker proteins of choice include, e.g., Green Fluorescent Protein (GFP;Clontech), CD64, or a CD64-GFP fusion protein. Flow cytometry (FCM), anautomated, laser optics-based technique, is used to identify transfectedcells expressing GFP or CD64-GFP and to evaluate the apoptotic state ofthe cells and other cellular properties. FCM detects and quantifies theuptake of fluorescent molecules that diagnose events preceding orcoincident with cell death. These events include changes in nuclear DNAcontent as measured by staining of DNA with propidium iodide; changes incell size and granularity as measured by forward light scatter and 90degree side light scatter; down-regulation of DNA synthesis as measuredby decrease in bromodeoxyuridine uptake; alterations in expression ofcell surface and intracellular proteins as measured by reactivity withspecific antibodies; and alterations in plasma membrane composition asmeasured by the binding of fluorescein-conjugated Annexin V protein tothe cell surface. Methods in flow cytometry are discussed in Ormerod, M.G. (1994; Flow Cytometry, Oxford, New York N.Y.).

[0390] The influence of VAP on gene expression can be assessed usinghighly purified populations of cells transfected with sequences encodingVAP and either CD64 or CD64-GFP. CD64 and CD64-GFP are expressed on thesurface of transfected cells and bind to conserved regions of humanimmunoglobulin G (IgG). Transfected cells are efficiently separated fromnontransfected cells using magnetic beads coated with either human IgGor antibody against CD64 (DYNAL, Lake Success N.Y.). mRNA can bepurified from the cells using methods well known by those of skill inthe art. Expression of mRNA encoding VAP and other genes of interest canbe analyzed by northern analysis or microarray techniques.

[0391] XV. Production of VAP Specific Antibodies

[0392] VAP substantially purified using polyacrylamide gelelectrophoresis (PAGE; see, e.g., Harrington, M. G. (1990) MethodsEnzymol. 182:488495), or other purification techniques, is used toimmunize animals (e.g., rabbits, mice, etc.) and to produce antibodiesusing standard protocols.

[0393] Alternatively, the VAP amino acid sequenceis analyzed usingLASERGENE software (DNASTAR) to determnine regions of highimmunogenicity, and a corresponding oligopeptide is synthesized and usedto raise antibodies by means known to those of skill in the art. Methodsfor selection of appropriate epitopes, such as those near the C-terminusor in hydrophilic regions are well described in the art (Ausubel et al.,supra, ch. 11).

[0394] Typically, oligopeptides of about 15 residues in length aresynthesized using an ABI 431A peptide synthesizer (Applied Biosysters)using FMOC chemistry and coupled to KLH (Sigrna-Aldrich, St. Louis Mo.)by reaction with N-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) toincrease immunogenicity (Ausubel et al., supra). Rabbits are immunizedwith the oligopeptide-KLH complex in complete Freund's adjuvant.Resulting antisera are tested for antipeptide and anti-VAP activity by,for example, binding the peptide or VAP to a substrate, blocking with 1%BSA, reacting with rabbit antisera, washing, and reacting withradio-iodinated goat anti-rabbit IgG.

[0395] XVI. Purification of Naturally Occurring VAP Using SpecificAntibodies

[0396] Naturally occurring or recombinant VAP is substantially purifiedby immunoaffinity chromatography using antibodies specific for VAP. Animmunoaffinity column is constructed by covalently coupling anti-VAPantibody to an activated chromatographic resin, such as CNBr-activatedSEPHAROSE (Amersham Biosciences). After the coupling, the resin isblocked and washed according to the manufacturer's instructions.

[0397] Media containing VAP are passed over the immunoaffinity column,and the column is washed under conditions that allow the preferentialabsorbance of VAP (e.g., high ionic strength buffers in the presence ofdetergent). The column is eluted under conditions that disruptantibody/VAP binding (e.g., a buffer of pH 2 to pH 3, or a highconcentration of a chaotrope, such as urea or thiocyanate ion), and VAPis collected.

[0398] XVII. Identification of Molecules Which Interact with VAP

[0399] VAP, or biologically active fragments thereof, are labeled with¹²⁵I Bolton-Hunter reagent (Bolton, A. E. and W. M. Hunter (1973)Biocheim J. 133:529-539). Candidate molecules previously arrayed in thewells of a multi-well plate are incubated with the labeled VAP, washed,and any wells with labeled VAP complex are assayed. Data obtained usingdifferent concentrations of VAP are used to calculate values for thenumber, affinity, and association of VAP with the candidate molecules.

[0400] Alternatively, molecules interacting with VAP are analyzed usingthe yeast two-hybrid system as described in Fields, S. and O. Song(1989; Nature 340:245-246), or using commercially available kits basedon the two-hybrid system, such as the MATCHMAKER system (Clontech).

[0401] VAP may also be used in the PATHCALLING process (CuraGen Corp.,New Haven Conn.) which employs the yeast two-hybrid system in ahigh-throughput manner to determine all interactions between theproteins encoded by two large libraries of genes (Nandabalan, K. et al.(2000) U.S. Pat. No. 6,057,101).

[0402] XVIII. Demonstration of VAP Activity

[0403] VAP activity is measured by its inclusion in coated vesicles. VAPcan be expressed by transforming a mammalian cell line such as COS7,HeLa, or CHO with an eukaryotic expression vector encoding VAP.Eukaryotic expression vectors are commercially available, and thetechniques to introduce them into cells are well known to those skilledin the art. A small amount of a second plasmid, which expresses any oneof a number of marker genes, such as O-galactosidase, is co-transformedinto the cells in order to allow rapid identification of those cellswhich have taken up and expressed the foreign DNA. The cells areincubated for 48-72 hours after transformation under conditionsappropriate for the cell line to allow expression and accumulation ofVAP and p-galactosidase.

[0404] Transformed cells are collected and cell lysates are assayed forvesicle formation. A non-hydrolyzable form of GTP, GTPγS, and an ATPregenerating system are added to the lysate and the mixture is incubatedat 37° C. for 10 minutes. Under these conditions, over 90% of thevesicles remain coated (Orci, L. et al (1989) Cell 56:357-368).Transport vesicles are salt-released from the Golgi membranes, loadedunder a sucrose gradient, centrifuged, and fractions are collected andanalyzed by SDS-PAGE. Co-localization of VAP with clathrin or COPcoatamer is indicative of VAP activity in vesicle formation. Thecontribution of VAP to vesicle formation can be confirmed by incubatinglysates with antibodies specific for VAP prior to GTPγS addition. Theantibody will bind to VAP and interfere with its activity, thuspreventing vesicle formation.

[0405] In the alternative, VAP activity is measured by its ability toalter vesicle trafficking pathways. Vesicle trafficking in cellstransformed with VAP is examined using fluorescence microscopy.Antibodies specific for vesicle coat proteins or typical vesicletrafficking substrates such as transferrin or the mannose-6-phosphatereceptor are commercially available. Various cellular components such asER, Golgi bodies, peroxisomes, endosomes, lysosomes, and the plasmalemmaare examined. Alterations in the numbers and locations of vesicles incells transformed with VAP as compared to control cells arecharacteristic of VAP activity.

[0406] Various modifications and variations of the describedcompositions, methods, and systems of the invention will be apparent tothose skilled in the art without departing from the scope and spirit ofthe invention. It will be appreciated that the invention provides noveland useful proteins, and their encoding polynucleotides, which can beused in the drug discovery process, as well as methods for using thesecompositions for the detection, diagnosis, and treatment of diseases andconditions. Although the invention has been described in connection withcertain embodiments, it should be understood that the invention asclaimed should not be unduly limited to such specific embodiments. Norshould the description of such embodiments be considered exhaustive orlimit the invention to the precise forms disclosed. Furthermore,elements from one embodiment can be readily recombined with elementsfrom one or more other embodiments. Such combinations can form a numberof embodiments within the scope of the invention. It is intended thatthe scope of the invention be defined by the following claims and theirequivalents. TABLE 1 Incyte Incyte Incyte Incyte Polypeptide PolypeptidePolynucleotide Polynucleotide Full Length Project ID SEQ ID NO: ID SEQID NO: ID Clones 7500521 1 7500521CD1 21 7500521CB1 6369107CA2,90033542CA2, 90116770CA2, 90118910CA2, 90119020CA2, 90119081CA2,90119090CA2, 90119101CA2, 90119173CA2, 90119202CA2, 90119257CA2,90119265CA2, 90119273CA2, 90119289CA2 7502992 2 7502992CD1 22 7502992CB190174555CA2, 90174563CA2, 90174571CA2, 90174579CA2, 90174587CA2,90174679CA2, 90174695CA2 71187173 3 71187173CD1 23 71187173CB12159469CA2 7503143 4 7503143CD1 24 7503143CB1 7503563 5 7503563CD1 257503563CB1 8017520CA2, 8017664CA2 6244251 6 6244251CD1 26 6244251CB17503467 7 7503467CD1 27 7503467CB1 6262711CA2, 90050304CA2, 90050312CA2,90050320CA2, 90050328CA2, 90050336CA2, 90050344CA2, 90050374CA2,90050404CA2, 90050412CA2, 90050420CA2, 90050428CA2, 90050436CA2,90050441CA2, 90050444CA2, 90050453CA2, 90050468CA2, 90050635CA2,90066560CA2 6599034 8 6599034CD1 28 6599034CB1 7504179 9 7504179CD1 297504179CB1 71249354 10 71249354CD1 30 71249354CB1 7505803 11 7505803CD131 7505803CB1 3524185CA2, 90179201CA2, 90179233CA2, 90179333CA2 750580412 7505804CD1 32 7505804CB1 7505846 13 7505846CD1 33 7505846CB190053747CA2, 90053755CA2 55004585 14 55004585CD1 34 55004585CB1 750601215 7506012CD1 35 7506012CB1 7506212 16 7506212CD1 36 7506212CB1 748180817 7481808CD1 37 7481808CB1 7488221 18 7488221CD1 38 7488221CB1 750589419 7505894CD1 39 7505894CB1 6262711CA2, 90050304CA2, 90050312CA2,90050320CA2, 90050328CA2, 90050336CA2, 90050344CA2, 90050374CA2,90050404CA2, 90050412CA2, 90050420CA2, 90050428CA2, 90050436CA2,90050441CA2, 90050444CA2, 90050468CA2, 90050635CA2, 90066560CA2 750590120 7505901CD1 40 7505901CB1 2702495CA2

[0407] TABLE 2 GenBank ID NO: Polypeptide Incyte or PROTEOME ProbabilitySEQ ID NO: Polypeptide ID ID NO: Score Annotation 1 7500521CD1 g72718679.4E−26 [Homo sapiens] golgi membrane protein GP73 Kladney, R. D. et al.(2000) GP73, a novel Golgi-localized protein upregulated by viralinfection. Gene 249: 53-65. 2 7502992CD1 g1163174 2.8E−24 [Rattusnorvegicus] similar to yeast Sec6p, Swiss-Prot Accession Number P32844;similar to mammalian B94, Swiss-Prot Accession Number Q03169; Method:conceptual translation supplied by author. Ting, A. E. et al. (1995)rSec6 and rSec8, mammalian homologs of yeast proteins essential forsecretion. Proc. Natl. Acad. Sci. USA 92: 9613-9617. 426545|SEC6 1.9E−25[Homo sapiens] [Plasma membrane] Protein with weak similarity to murineTnfip2, which is a tumor necrosis factor alpha(TNF)-induced protein.Charron, A. J. et al. (2000) Compromised cytoarchitecture and polarizedtrafficking in autosomal dominant polycystic kidney disease cells. J.Cell Biol. 149: 111-124. 3 71187173CD1 g7920147 0.0 [Homo sapiens]N-ethylmaleimide-sensitive factor 623572|NSF 0.0 [Homo sapiens][Hydrolase; ATPase] N-ethylmaleimide-sensitive factor, an ATPaseinvolved in membrane fusion during exocytosis. Hoyle, J. et al. (1996)Localization of human and mouse N-ethylmaleimide- sensitive factor (NSF)gene: a two-domain member of the AAA family that is involved in membranefusion. Mamm. Genome 7: 850-852. 4 7503143CD1 g13752411 3.4E−291 [Homosapiens] TOB3 598630|FLJ10709 1.8E−294 [Homo sapiens] [Hydrolase;Protease (other than proteasomal); ATPase] [Cytoplasmic; Mitochondrial]Member of the ATPases associated with various cellular activities (AAA)protein family, has low similarity to SPG7 (paraplegin), which is anuclear-encoded mitochondrial metalloprotease associated with hereditaryspastic paraplegia (HSP). 5 7503563CD1 g13938372 7.5E−81 [Homo sapiens]SNARE protein 567962|YKT6 6.5E−82 [Homo sapiens] [Docking protein][Golgi; Endoplasmic reticulum; Secretory vesicles; Cytoplasmic; Plasmamembrane] SNARE protein required for vesicle transport between theendoplasmic reticulum and Golgi. McNew, J. A. et al. (1997) Ykt6p, aprenylated SNARE essential for endoplasmic reticulum-Golgi transport. J.Biol. Chem. 272: 17776-17783. 6 6244251CD1 g8099669 0.0 [Homo sapiens]golgin-like protein Gilles, F. et al. (2000) Cloning andcharacterization of a Golgin-related gene from the large-scalepolymorphism linked to the PML gene. Genomics 70: 364-374. 599670|GLP0.0 [Homo sapiens] Protein with moderate similarity to GOLGA2(Golgin-95), which is a Golgi protein with leucine zipper and glutamate-and proline-rich tracts, and an autoantigen in some autoimmunedisorders. Gilles, F. et al. (2000), supra. 7 7503467CD1 g36416747.6E−40 [Homo sapiens] gammal-adaptin Takatsu, H. et al. (1998)Identification and characterization of novel clathrin adaptor-relatedproteins. J. Biol. Chem. 273: 24693-24700. 334094|AP1G1 6.7E−41 [Homosapiens] [Vesicle coat protein] [Golgi; Cytoplasmic] Gamma-adaptin 1, amember of the adaptin family of proteins, promotes the formation ofclathrin coated vesicles and pits, involved in intracellular transport.Peyrard, M. et al. (1998) Cloning, expression pattern, and chromosomalassignment to 16q23 of the human ganmia-adaptin gene (ADTG). Genomics50: 275-280. Takatsu, H. et al. (1998), supra. 8 6599034CD1 g58704263.0E−130 [Homo sapiens] epsilon-COP protein 428378|COPE 1.1E−130 [Homosapiens] Coatomer protein complex subunit epsilon (human leucocytevacuolar sorting protein), a putative component of the coatomer complex(COPI), may be involved in vesicle transport, may have clinicalsignificance in inflammatory mediator release. Guo, Q. et al. (1994)Disruptions in Golgi structure and membrane traffic in a conditionallethal mammalian cell mutant are corrected by epsilon-COP. J. Cell Biol.125: 1213-1224 Rajasekariah, P. et al. (1999) Molecular cloning andcharacterization of a cDNA encoding the human leucocyte vacuolar proteinsorting (h1Vps45). Int. J. Biochem. Cell Biol. 31: 683-694. 9 7504179CD1g202928 6.4E−45 [Rattus norvegicus] clathrin-associated protein 17Kirchhausen, T. et al. (1991) AP17 and AP19, the mammalian small chainsof the clathrin-associated protein complexes show homology to Yap17p,their putative homolog in yeast. J. Biol. Chem. 266: 11153-11157.340214|AP2S1 6.40E−45 [Homo sapiens] [Vesicle coat protein][Endosome/Endosomal vesicles; Secretory vesicles; Cytoplasmic; Plasmamembrane] Adaptor-related protein complex 2 sigma 1 subunit, associatedwith clathrin coated vesicles and involved in intracellular transport.Winterpacht, A. et al. (1996) Human CLAPS2 encoding AP17, a small chainof the clathrin-associated protein complex: cDNA cloning and chromosomalassignment to 19q13.2-q13.3. Cytogenet. Cell Genet. 75: 132-135Holzmann, K. et al. (1998) A novel spliced transcript of human CLAPS2encoding a protein alternative to clathrin adaptor protein AP17. Gene220: 39-44. 10 71249354CD1 g2792500 0.0 [Rattus norvegicus] clathrinassembly protein short form Kim, H.-L. and Lee, S.-C. (1999) Exp. Mol.Med. 31: 191-196. 298495|PICALM 6.4E−219 [Homo sapiens] [Complexassembly protein] Clathrin assembly lymphoid myeloid leukemia protein,binds to clathrin heavy chain (CLTC) and plays a role in coated pitinternalization; rearrangements in the corresponding gene are associatedwith acute lymphoblastic and acute myeloid leukemias. Vecchi, M. et al.(2001) J. Cell. Biol. 153: 1511-1517. Tebar, F. et al. (1999) Mol. Biol.Cell. 10: 2687-2702. 333520|Rn. 10888 8.4E−217 [Rattus norvegicus][Complex assembly protein] Clathrin assembly lymphoid myeloid leukemiaprotein, plays a role in coated pit internalization; rearrangements inthe corresponding human CALM gene are associated with acutelymphoblastic and acute myeloid leukemias. Kim, H.-L., and Kim, J. A.(2000) Exp. Mol. Med. 32: 222-226. Kim, H.-L. and Lee, S.-C. (1999),supra. 11 7505803CD1 g2791806 1.8E−21 [Mus musculus] bet3 323780|Bet31.6E−22 [Mus musculus] Protein with high similarity to S. cerevisiaeBET3, which is a low molecular weight subunit of Transport ProteinParticle (TRAPP) complex that is involved in targeting and fusion of ERto Golgi transport vesicles. 12 7505804CD1 g5917668 5.4E−70 [Homosapiens] cysteine-rich hydrophobic 2 CHIC2 Cools, J. et al. (1999) Blood94: 1820-1824. 429060|CHIC2 4.7E−71 [Homo sapiens] Cysteine-richhydrophobic protein; corresponding gene is at a translocation breakpointand undergoes fusion to ETV6 in acute myeloid leukemias. Cools, J. etal. (1999), supra. Cools, J. et al. (2001) FEBS Lett. 492: 204-209.368616|Chic1 3.2E−42 [Mus musculus] Cysteine-rich hydrophobic domain 1,may playa role in brain development; corresponding gene is located inthe X-inactivation center and is subject to X-inactivation Simmler, M.C. et al. (1997) Mamm. Genome 8: 760-766. 13 7505846CD1 g1373146 4.9E−65[Homo sapiens] CALM Dreyling, M. H. et al. (1996) Proc. Natl. Acad. Sci.USA 93: 4804-4809. 298495|PICALM 4.2E−66 [Homo sapiens] [Complexassembly protein] Clathrin assembly lymphoid myeloid leukemia protein,binds to clathrin heavy chain (CLTC) and plays a role in coated pitinternalization; rearrangements in the corresponding gene are associatedwith acute lymphoblastic and acute myeloid leukemias. Vecchi, M. et al.(2001), supra. Tebar, F. et al. (1999), supra. 333520|Rn. 10888 1.4E−65[Rattus norvegicus] [Complex assembly protein] Clathrin assemblylymphoid myeloid leukemia protein, plays a role in coated pitinternalization; rearrangements in the corresponding human CALM gene areassociated with acute lymphoblastic and acute myeloid leukemias. Kim,H.-L. and Kim, J. A. (2000), supra. Kim, H.-L. and Lee, S.-C. (1999),supra. 14 55004585CD1 g10180266 0.0 [Mus musculus] LBA Wang, J. W. etal. (2001) J. Immunol. 166: 4586-4595. 698261|LRBA 0.0 [Homo sapiens]Lipopolysaccharide-responsive and beige-like anchor, a putativeprotein-binding protein that contains WD-like repeats and a BEACH (BEigeAnd CHS) domain, may play a role in vesicle transport. Wang, J. W. etal. (2001), supra. 242600|F10F2.1 0.0 [Caenorhabditis elegans] Proteinwith a WD domain and a G-beta repeat; has a region with high similarityto S. cerevisiae Bph1p. Shea, J. E. et al. (1994) Nucleic Acids Res. 22:5555-5564. 15 7506012CD1 g1929347 2.4E−202 [Homo sapiens]mu-adaptin-related protein 2 Wang, X. and Kilimann, M. W. (1997) FEBSLett. 402: 57-61. 743530|AP4M1 8.1E−204 [Homo sapiens] [Vesicle coatprotein] [Golgi; Cytoplasmic; Other vesicles of the secretory/endocyticpathways] Adaptor-related protein complex 4 mu 1 subunit, member of theclathrin adaptor complex medium chain (mu) family, interacts withtyrosine-based sorting signals and is involved in Golgi to endosomeprotein trafficking. Wang, X. and Kilimann, M. W. (1997), supra.Aguilar, R. C. et al. (2001) J. Biol. Chem. 276: 13145-13152.580887|Ap1m1 4.3E−38 [Mus musculus] [Vesicle coat protein] [Golgi;Secretory vesicles; Cytoplasmic] Medium chain 1 of theclathrin-associated protein complex Ap-1, a member of the medium chainfamily of the clatherin adapter complex that is involved inintracellular protein transport. Folsch, H. et al. (2001) J. Cell Biol.152: 595-606. 16 7506212CD1 g5733726 0.0 [Homo sapiens] (AF169548)gamma-synergin Page, L. J. et al. (1999) J. Cell Biol. 146: 993-1004.428468|AP1GBP1 0.0 [Homo sapiens] [Golgi; Secretory vesicles;Cytoplasmic] AP1 gamma subunit binding protein 1, interacts withgamma-adaptins (AP1G1 and AP1G2) and the AGEH domains of GGA proteins(GGA1, KIAA1080, KIAA0154), may be involved in intracellular proteintrafficking. Page, L. J. et al. (1999), supra. 712809|Ap1gbp1 1.2E−219[Rattus norvegicus] AP1 gamma subunit binding protein 1, interacts withgamma- adaptin (Ap1g1) and Scamp1, may be involved in intracellularprotein trafficking. Fernandez-Chacon, R. et al. (2000) Biol. Chem. 275:12752-12756. 17 7481808CD1 g10801596 8.0E−161 [Mus musculus] Doc2gammaFukuda, M. and Mikoshiba, K. (2000) Biochem. Biophys. Res. Commun. 276:626-632. 624062|Doc2g 6.7E−162 [Mus musculus] [Small molecule-bindingprotein] Double C2 protein gamma, contains a Munc13-1 interacting domain(Mid) and two C2 domains, a possible effector for Munc13-1 and may helpregulate vesicular trafficking, highly expressed in heart. Fukuda, M.and Mikoshiba, K. (2000), supra. 570448|KIAA0985 4.5E−91 [Homo sapiens][Small molecule-binding protein] [Secretory vesicles; Cytoplasmic;Plasma membrane] Rabphilin-3A, a Ca2+ and phospholipid binding synapticvesicle protein that may be involved in intracellular transport andneurotransmitter release; may be a target for Rab3A small GTP bindingprotein. Orita, S. et al. (1995) Biochem. Biophys. Res. Commun. 206:439-448. 18 7488221CD1 g2827162 0.0 [Rattus norvegicus] rsec15 Kee, Y.et al. (1997) Proc. Natl. Acad. Sci. USA 94: 14438-14443. 609871|Sec150.0 [Rattus norvegicus] Rat SEC15, a subunit of the mammalian exocystcomplex, may have a role in exocytosis and vesicle fusion. Kee, Y. etal. (1997), supra. 563627|SEC15L 0.0 [Homo sapiens] Protein with strongsimilarity to rat Sec15, which is a subunit of the exocyst complex thatmay have a role in vesicle fusion. 19 7505894CD1 g3641674 8.1E−40 [Homosapiens] gamma1-adaptin Takatsu, H. et al. (1998), supra. 746241|Ap1g16.8E−41 [Mus musculus] Gamma-adaptin 1, subunit of the Golgi adaptor,which links clathrin to transmembrane proteins in coated pits andvesicles. Robinson, M. S. et al. (1990) J. Cell. Biol. 111: 2319-2326.334094|AP1G1 6.9E−41 [Homo sapiens] [Vesicle coat protein] [Golgi;Cytoplasmic] Adaptor-related protein complex 1 gamma 1 subunit, promotesthe formation of clathrin coated vescicles and pits for intracellulartransport; deletion of the corresponding gene occurs in Wilm's tumor,prostate adenocarcinomas, and hepatocelluar carcinomas. Takatsu, H. etal. (1998), supra. 20 7505901CD1 g12803245 2.6E−100 [Homo sapiens]syntaxin 4A (placental) 341314|STX4A 1.2E−100 [Homo sapiens] Syntaxin 4,broadly expressed target SNAP receptor (t-SNARE), involved in targetingand exocytosis of a variety of secretory vesicles, interacts withSNAP23, regulates alpha granule release in platelets. Cabaniols, J. P.et al. (1999) Mol. Biol. Cell. 10: 4033-4041. 581533|Stx4a 6.8E−98 [Musmusculus] [Cytoplasmic] Syntaxin 4, broadly expressed target SNAPreceptor (t-SNARE), involved in targeting and exocytosis of a variety ofsecretory vesicles via interactions with Vamp2, Snap23, Dnajc5, andother proteins, regulates glucose transporter 4 (Slc2a4) trafficking.Olson, A. L. et al. (1997) Mol. Cell. Biol. 17: 2425-2435. 705044|Stx4a1.4E−97 [Rattus norvegicus] [Vesicle coat protein; Docking protein][Basolateral plasma membrane; Unspecified membrane] Syntaxin 4, broadlyexpressed target SNAP receptor (t-SNARE), involved in targeting andexocytosis of a variety of secretory vesicles via interactions withVamp2, Rab4, and other proteins; upregulated in an insulin-resistantdiabetic model. Maier, V. H. et al. (2000) Diabetes 49: 618-625.

[0408] TABLE 3 SEQ Potential Potential ID Amino Acid PhosphorylationGlycosylation Analytical NO: Incyte Polypeptide ID Residues Sites SitesSignature Sequences, Domains and Motifs Methods and Databases 17500521CD1 380 S36 S68 S92 S277 N115 N150 signal_cleavage: M1-A29 SPSCANS328 T76 T195 T312 Signal Peptide: M1-A29 HMMER Cytosolic domain: M1-R12TMHMMER Transmembrane domain: L13-I35 Non-cytosolic domain: S36-L380 27502992CD1 326 S75 S110 S165 signal_cleavage: M1-A55 SPSCAN S195 Y137PROTEIN B94 TUMOR NECROSIS FACTOR BLAST_PRODOM INDUCED PRIMARY RESPONSEPD025051: L92-G243 Leucine zipper pattern: L176-L197, L183-L204 MOTIFS 371187173CD1 744 S139 S356 S437 N190 N435 ATPase family associated withvarious cellular activities HMMER_PFAM S460 S531 S547 (AAA): G255-N454,S538-S717 S647 S739 T48 T114 T166 T373 T411 T461 T476 T494 T579 T646Y112 Y593 Cell division protein 48 (CDC48), domain 2: E98-F185HMMER_PFAM Cell division protein 48 (CDC48), N-terminal: A2-D86HMMER_PFAM AAA-protein family proteins BLIMPS_BLOCKS BL00674: Q353-D399,N435-N454, V174-N194, V253-G274, G296-G338 AAA-protein family signature:D348-V424 PROFILESCAN PROTEIN VESICULAR FUSION FUSION BLAST_PRODOMTRANSPORT ENDOPLASMIC RETICULUM GOLGI STACK ATP-BINDING REPEAT PD006896:A2-K254; PD006245: L609-G737 PROTEIN ATP-BINDING PROTEASE SUBUNITBLAST_PRODOM HOMOLOG REPEAT CELL DIVISION ATP- DEPENDENT NUCLEARPD000092: V285-M453 PROTEIN FUSION VESICULAR FUSION N- BLAST_PRODOMETHYLMALEIMIDE-SENSITIVE TRANSPORT ENDOPLASMIC RETICULUM GOLGI STACKATP-BINDING PD006817: V539-L608 AAA-PROTEIN FAMILY BLAST_DOMODM02248|P46459|2-210: A2-P211 DM02248|P18708|2-210: A2-P211DM02248|P46460|2-210: A2-P211 AAA-PROTEIN FAMILY BLAST_DOMODM00024|P18708|212-383: D212-L384 AAA-protein family signature:I367-R385 MOTIFS 4 7503143CD1 648 S48 S225 S263 N266 N341 N400 ATPasefamily associated with various cellullar activities HMMER_PFAM S304 S369S402 (AAA): N347-A543 S444 S465 S516 S526 S629 T53 T118 T173 T221 T242T288 T292 T338 T356 T377 T401 T422 T612 Y70 AAA-protein family proteinsBLIMPS_BLOCKS BL00674: Y345-A366, G378-R420, L433-E479, G524-A543PROTEIN ATPase-LIKE F54B3.3 BLAST_PRODOM PD034475: R219-N347 TROPOMYOSINBLAST_DOMO DM00077|P37709|1104-1277: E56-K214 TRICHOHYALIN BLAST_DOMODM03839|P37709|632-1103: E66-R227 AAA-PROTEIN FAMILY BLAST_DOMODM00024|P25694|208-367: R346-I463 ATP/GTP-binding site motif A (P-loop):G352-T359 MOTIFS Growth factor and cytokines receptors family signature1: MOTIFS C606-W618 5 7503563CD1 164 S35 S51 S58 T92 N72 Synaptobrevin:G54-Q143 HMMER_PFAM PROTEIN SNARE YKT6 PRENYLATED BLAST_PRODOMTRANSMEMBRANE YKT6P ISOPRENYLATED V-SNARE B0361.8 CHROMOSOME PD010770:M1-K53 6 6244251CD1 702 S53 S94 S191 S221 N463 Myosin tail: Q468-K493HMMER_PFAM S274 S295 S320 S455 S491 S517 S541 S682 T12 T51 T112 T144T204 T256 T373 T579 GOLGI STACK COILED COIL GOLGIN 95 CIS- BLAST_PRODOMGOLGI MATRIX PROTEIN GM130 SIMILAR PD033411: F542-D701 PROTEINCOILED-COIL CHAIN MYOSIN REPEAT BLAST_PRODOM HEAVY ATP-BINDING FILAMENTHEPTAD PD000002: R240-L480, E298-E484, Q217-K464, V196-L445, L330-E560,Q167-L409, R149-R396 GOLGIN 95 GOLGI STACK COILED-COIL BLAST_RODOMPD173178: E220-M282 CIS-GOLGI MATRIX PROTEIN GM130 GOLGI BLAST_PRODOMSTACK COILED-COIL PD180737: H626-D701 TRICHOHYALIN BLAST_DOMODM03839|P37709|632-1103: I84-E484, Q68-E478, E103-E484, Q68-R479,R70-E478 DM03839|P22793|921-1475: T144-K609, E90-R479, Q87-E484,R70-E537, Q87-R479, Q68-R436, L210-R479 DM03839||Q07283|91-443:Q182-E484, Q182-L449, P66-E400 TROPOMYOSIN BLAST_DOMODM00077|P37709|1104-1277: E298-Q448, L330-E484, E343-E484, R242-Q433Leucine zipper pattern: L360-L381, L367-L388, L374-L395, MOTIFSL381-L402, L388-L409, L395-L416, L402-L416, L409-L423, L416-L430 77503467CD1 137 S37 S76 T13 T16 Adaptin N terminal region: E23-V85HMMER_PFAM T19 T44 T80 Y45 PROTEIN COATED SUBUNIT PITS COMPLEXBLAST_PRODOM ADAPTIN ALPHA-ADAPTIN CLATHRIN ASSEMBLY LARGE PD001921:L7-I84 ADAPTIN; GAMMA; YPR029C; ALPHA BLAST_DOMO DM03711|P22892|2-804:A3-A126, I84-A121 DM03711|S49876|5-840: L7-I84, T92-G119DM03711|S54503|1-816: L7-I84, S76-A121 8 6599034CD1 256 S44 S77 S95 S99N116 COATOMER EPSILON SUBUNIT PROTEIN EPSILON BLAST_PRODOM T218 COATEPSILON-COP TRANSPORT GOLGI STACK MEMBRANE PD017726: D17-T193, S190-A2569 7504179CD1 92 T62 Clathrin adaptor complex small chain: M1-E92HMMER_PFAM Insulin family signature: D25-K80 PROFILESCAN PROTEINCLATHRIN ASSEMBLY SUBUNIT COAT BLAST_PRODOM SMALL CHAIN ADAPTOR COATEDPITS PD003841: F2-E92 CLATHRIN ADAPTOR COMPLEXES SMALL CHAIN BLAST_DOMODM02291|P53680|1-141: F2-E92 DM02291|Q00381|1-146: K6-E92DM02291|P35181|1-145: F2-E92 DM02291|Q09905|1-145: K6-L82 Clathrinadaptor complexes small chain signature: MOTIFS I7-F17 10 71249354CD1610 S5 S62 S128 S137 N69 N105 N384 ENTH (Epsin N-terminal homology)domain: G19-V141 HMMER_PFAM S273 T7 T30 T161 N445 N505 N513 T317 T386T507 T508 T523 PROTEIN CLATHRIN ASSEMBLY COAT AP180 BLAST_PRODOMASSOCIATED COATED PITS ALTERNATIVE SPLICING PD014599: G420-W528,A358-H402, L354-G419 PD009526: Q4-R139 PROTEIN ASSEMBLY CLATHRIN COATAP180 BLAST_PRODOM ASSOCIATED COATED PITS ALTERNATIVE SPLICING PD005811:M156-K291 PROTEIN CLATHRIN ASSEMBLY FORM CALM BLAST_PRODOM SHORT LONGTYPE I PD152556: Q529-M610 Cell attachment sequence: R261-D263 MOTIFS 117505803CD1 53 S11 T27 BET3 PROTEIN CCP1 MET1 INTERGENIC REGIONBLAST_PRODOM ZK1098.5 CHROMOSOME III PD016734: K13-E53, M1-M14 127505804CD1 137 S44 S109 T56 T83 Fungal Zn(2)-Cys(6) binuclear clusterdomain proteins BLIMPS_BLOCKS BL00463: C103-E114 13 7505846CD1 130 S5S62 T7 T30 N69 ENTH domain: G19-M130 HMMER_PFAM PROTEIN CLATHRINASSEMBLY COAT AP180 BLAST_PRODOM ASSOCIATED COATED PITS ALTERNATIVESPLICING PD009526: Q4-R114 PROTEIN CLATHRIN ASSEMBLY FORM CALMBLAST_PRODOM SHORT LONG TYPE I PD152556: T81-M130 14 55004585CD1 2852S34 S61 S121 S278 N163 N335 N851 Signal Peptide: M46-V60 HMMER S326 S435S508 N966 N992 N1013 S535 S653 S730 N1040 N1217 S810 S993 S999 N1310N1346 S1005 S1015 S1084 N1572 N1741 S1086 S1100 S1118 N1793 N2199 S1231S1299 S1337 S1412 S1488 S1562 S1568 S1574 S1590 Beige/BEACH domain:T2201-R2478 HMMER_PFAM S1599 S1605 S1617 S1753 S1795 S1849 S2028 S2039S2053 S2054 S2132 S2187 S2190 S2210 S2225 S2279 S2339 S2378 S2446 S2608T14 T26 T165 T259 T389 T607 T620 T637 T686 T1014 T1033 T1068 T1074 T1163T1167 T1216 T1251 T1253 T1340 WD domain, G-beta repeat: P2678-S2714,L2579-S2613, HMMER_PFAM T1426 T1466 L2761-R2795, L2619-Y2659,Q2802-Y2838 T1566 T1654 T1797 T1887 T1962 T2003 T2008 T2011 T2017 T2089T2140 T2161 T2183 T2201 T2240 T2388 T2490 T2616 T2683 T2785 Y319 Y891Y2232 PROTEIN TRANSPORT FAN FACTOR ASSOCIATED BLAST_PRODOM WITH NSMASEACTIVATION REPEAT WD PD007848: G2175-R2478, E2275-F2534, Y2094-R2192,V2630-L2655 CDC4-LIKE PROTEIN BLAST_PRODOM PD148854: L764-R910,P252-G383, Q360-S710, K885-S1086, V2405-G2569, S1859-L1877 Cellattachment sequence: R1467-D1469 MOTIFS Prokaryotic membrane lipoproteinlipid attachment site: MOTIFS L263-C273 15 7506012CD1 385 S9 S10 S77S108 N134 Adaptor complexes medium subunit family: F5-I385 HMMER_PFAMS109 S114 S154 S198 S240 S280 S376 T38 T57 Y34 Clathrin adaptorcomplexes medium chain proteins BLIMPS_BLOCKS BL00990: G25-L62,P105-N134, E184-Q217, A366-R384 Clathrin coat assembly protein signatureBLIMPS_PRINTS PR00314: G12-L32, L107-G135, V182-G209, L254-P269 tRNAsynthetases class I BLIMPS_PFAM PF00587: G144-F151 PROTEIN MEDIUM CHAINCOATED PITS BLAST_PRODOM CLATHRIN COAT ASSEMBLY SUBUNIT COMPLEXPD002289: I16-I385, F6-M49 CLATHRIN ADAPTOR COMPLEXES MEDIUM BLAST_DOMOCHAIN DM01702|P54672|1-438: V48-I385, M1-V47 DM01720|P35602|2-421:P98-I385, V48-P75, S3-D23 DM01702|Q09718|1-445: V48-I385, M1-F33DM01702|P35603|1-440: V48-R384, M1-D23 Cell attachment sequence: R21-D23MOTIFS 16 7506212CD1 1269 S155 S164 S199 N67 N221 N263 S213 S234 S235N268 N295 N343 S270 S469 S473 N624 N699 N737 S483 S557 S580 N893 N1101S627 S665 S742 S769 S772 S781 S789 S792 S809 S854 S921 S984 S990 S1005S1024 S1030 S1150 S1213 S1230 S1234 T257 T314 T318 T351 T365 T639 T731T743 T803 T886 T944 T971 T1055 T1136 T1177 Y356 Y940 17 7481808CD1 394S15 S194 S236 C2 domain: L267-Q355, L101-V181 HMMER_PFAM S338 T141 T160T168 T346 SMRT_C2 protein kinase C conserved region 2 domain: HMMER_SMRTA100-D214, G266-E380 Inositol monophosphatase family proteinsBLIMPS_BLOCKS BL00629: L114-Y122 C2 domain signature and profile:V254-V308 PROFILESCAN C2 domain signature and profile: L88-V142PROFILESCAN C2 domain signature BLIMPS_PRINTS PR00360: K311-S324,L335-D343, A282-L294 Synaptotagmin signature BLIMPS_PRINTS PR00399:V254-V269, V269-A282, P326-D341 C2-DOMAIN BLAST_DOMODM00150|Q06846|558-683: E249-L372 DM00150|JC2473|249-373: E249-L372DM00150|Q06846|402-526: L85-E218, G252-G352 DM00150|P41885|873-1006:E249-L372 C2 domain signature: C274-F289 MOTIFS 18 7488221CD1 804 S35S150 S196 N124 N256 N425 PROTEIN OF THE RSEC15 SUBUNIT FINAL STEPBLAST_PRODOM S206 S211 S263 N553 N570 N573 SECRETORY PATHWAY T14P8.16S499 S509 S623 PD044053: L18-L721, I601-R794 S766 T10 T32 T85 T97 T127T276 T384 T511 T521 T555 T581 T589 T621 T757 T765 Y445 Y602 197505894CD1 137 S37 S76 T13 T16 Adaptin N terminal region: E23-V85HMMER_PFAM T19 T44 T80 Y45 PROTEIN COATED SUBUNIT PITS COMPLEXBLAST_PRODOM ADAPTIN ALPHA-ADAPTIN CLATHRIN ASSEMBLY LARGE PD001921:L7-I84 ADAPTIN; GAMMA; YPR029C; ALPHA BLAST_DOMO DM03711|P22892|2-804:A3-A126 DM03711|S49876|5-840: L7-I84, T92-G119 DM03711|S54503|1-816:L7-I84, S76-A121 20 7505901CD1 262 S14 S15 S36 S134 Syntaxin: M1-A253HMMER_PFAM S169 S181 S212 T31 T47 T194 T226 Y80 SMRT_t_SNARE: Helicalregion found in SNARES: HMMER_SMRT V160-A227 SMRT_SynN: R33-V118HMMER_SMRT Cytosolic domain: M1-K238 TMHMMER Transmembrane domain:V239-V261 Non-cytosolic domain: G262-G262 Syntaxin/epimorphin familyproteins BLIMPS_BLOCKS BL00914: R171-G220 SYNTAXIN COILED-COILTRANSMEMBRANE BLAST_PRODOM TRANSPORT NEUROTRANSMITTER PROTEIN 1ANEURON-SPECIFIC ANTIGEN PD001014: D3-I256 EPIMORPHIN FAMILY BLAST_DOMODM01996|S52726|32-297: E17-G262 DM01996|JU0136|23-288: D3-V260DM01996|P32856|23-287: S36-V260 DM01996|D48213|26-289: I48-V260Syntaxin/epimorphin family signature: R171-I210 MOTIFS

[0409] TABLE 4 Polynucleotide SEQ ID NO:/ Incyte ID/ Sequence LengthSequence Fragments 21/7500521CB1/2251 1-496, 13-242, 13-323, 13-562,13-577, 21-613, 26-625, 29-477, 29-779, 30-612, 35-272, 42-538, 69-758,80-714, 98-592, 100-748, 100-757, 100-787, 100-789, 100-888, 100-894,100-895, 100-918, 100-921, 100-930, 100-974, 103-921, 170-608, 177-736,182-805, 199-862, 233-772, 233-863, 268-891, 280-2251, 287-922, 319-862,323-502, 323-764, 338-817, 340-547, 340-584, 340-806, 340-828, 340-910,344-563, 356-1001, 380-1055, 380-1056, 380-1111, 380-1135, 380-1150,380-1172, 380-1195, 381-883, 381-1059, 381-1124, 381-1141, 381-1232,382-1065, 383-1151, 402-1062, 451-1047, 481-717, 513-804, 537-1238,591-1239, 596-1226, 604-875, 604-932, 615-875, 622-865, 653-1142,694-1267, 700-996, 720-1024, 732-874, 806-1065, 809-1017, 809-1024,809-1029, 809-1378, 858-1121, 959-1693, 977-1256, 977-1604, 1003-1287,1006-1815, 1008-1815, 1011-1818, 1042-1864, 1084-1654, 1137-1391,1137-1684, 1142-1387, 1157-1721, 1199-1526, 1331-2017, 1376-1543,1380-1842, 1380-1945, 1382-1736, 1397-1629, 1397-1647, 1414-1710,1520-1786, 1549-2251, 1550-1829, 1555-1872, 1609-1851, 1647-1968,1701-1862, 1718-1989, 1729-1851, 1738-1851, 1738-1996, 1762-1846,1781-2036, 1781-2067 22/7502992CB1/ 1-587, 1-594, 293-673, 437-962,524-793, 596-1055, 881-1567, 998-1230, 1024-1314, 1115-1457, 1190-1434,1190-1775, 1775 1191-1333, 1191-1432, 1191-1564, 1191-1586, 1191-1619,1191-1703, 1191-1711, 1191-1722, 1191-1734, 1191-1751, 1191-1770,1191-1773, 1191-1774, 1191-1775, 1194-1775, 1195-1775, 1202-1487,1215-1763, 1292-1775, 1297-1468, 1298-1775, 1337-1584, 1337-1775,1340-1629, 1341-1602, 1345-1485, 1370-1774 23/71187173CB1/ 1-452, 1-653,2-564, 6-522, 9-437, 9-774, 10-278, 10-536, 17-588, 17-693, 18-534,19-271, 20-615, 23-242, 23-516, 3959 23-658, 24-244, 25-175, 28-625,29-658, 31-819, 40-241, 40-406, 46-311, 46-334, 46-347, 47-928, 48-398,51-597, 51-629, 55-441, 61-142, 117-760, 385-679, 385-834, 385-933,411-1127, 420-1011, 469-709, 472-976, 485-736, 553-827, 580-1207,632-843, 675-1266, 692-1331, 696-1319, 707-1319, 745-1024, 763-1384,767-1247, 777-1331, 777-1502, 809-1046, 814-1038, 814-1422, 850-1579,854-1541, 870-1407, 894-1500, 897-1475, 912-1527, 940-1192, 997-1674,1005-1623, 1009-1279, 1027-1291, 1028-1652, 1031-1596, 1037-1691,1056-1442, 1063-1324, 1068-1767, 1092-1742, 1094-1726, 1096-1785,1110-1425, 1118-1542, 1132-1447, 1139-1760, 1177-1437, 1179-1705,1185-1744, 1196-1887, 1197-1757, 1198-1473, 1227-1789, 1278-1939,1280-1918, 1283-1942, 1299-2040, 1304-1909, 1304-1983, 1360-1914,1363-1776, 1409-2013, 1417-1654, 1421-1964, 1443-2090, 1444-1703,1444-1710, 1444-1954, 1445-1984, 1451-2055, 1456-2075, 1485-2045,1491-2146, 1504-1878, 1528-2179, 1534-2254, 1546-2074, 1555-2177,1557-2225, 1565-1746, 1568-2165, 1579-2124, 1583-1983, 1587-2165,1603-2326, 1605-2243, 1621-1893, 1639-2231, 1641-1928, 1703-1940,1706-1962, 1715-1975, 1719-2318, 1721-2001, 1721-2153, 1721-2381,1737-2222, 1761-2416, 1762-1955, 1762-1964, 1768-2417, 1775-2037,1781-2277, 1794-2042, 1816-2333, 1832-2378, 1841-2015, 1844-2109,1850-2045, 1868-2394, 1872-2440, 1912-2022, 1922-2142, 1926-2173,1941-2177, 1944-2220, 1950-2476, 1966-2439, 1976-2623, 1996-2464,2005-2355, 2006-2531, 2068-2446, 2084-2454, 2093-2609, 2104-2397,2118-2356, 2118-2358, 2118-2360, 2119-2735, 2152-2704, 2163-2256,2169-2789, 2179-2572, 2190-2664, 2194-2458, 2202-2441, 2202-2442,2202-2817, 2225-2468, 2233-2758, 2234-2758, 2257-2564, 2263-2799,2267-2718, 2274-2838, 2290-2539, 2301-2640, 2301-2847, 2310-3028,2310-3049, 2317-2599, 2317-2881, 2318-2574, 2319-2570, 2324-2768,2349-2809, 2366-3126, 2380-2624, 2386-2921, 2389-2627, 2391-2651,2421-2775, 2454-2737, 2455-3119, 2476-3022, 2481-3047, 2498-2778,2503-3042, 2504-2794, 2504-2817, 2529-2764, 2540-2920, 2573-2876,2580-2828, 2580-3161, 2581-2826, 2586-3247, 2605-3258, 2606-3098,2679-2928, 2700-2993, 2705-3347, 2713-3340, 2718-3260, 2719-3453,2768-3338, 2772-3047, 2772-3060, 2784-3267, 2795-3313, 2796-3353,2805-3453, 2812-3126, 2826-3362, 2839-3374, 2881-3334, 2886-3448,2889-3336, 2889-3338, 2889-3370, 2898-3483, 2901-3165, 2904-3529,2920-3497, 2931-3171, 2948-3390, 2950-3470, 2954-3478, 2962-3609,2967-3209, 2967-3321, 2967-3547, 2968-3215, 2977-3271, 2991-3238,2991-3252, 2998-3531, 3002-3391, 3028-3280, 3093-3757, 3099-3504,3112-3843, 3121-3890, 3133-3874, 3134-3418, 3153-3369, 3175-3603,3194-3709, 3206-3791, 3211-3866, 3215-3643, 3215-3646, 3215-3666,3215-3680, 3218-3459, 3218-3709, 3223-3427, 3223-3726, 3225-3750,3227-3837, 3229-3886, 3230-3890, 3233-3924, 3243-3592, 3247-3908,3252-3877, 3267-3895, 3271-3534, 3283-3543, 3293-3904, 3303-3890,3330-3597, 3340-3845, 3363-3959, 3371-3881, 3382-3938, 3403-3611,3407-3670, 3410-3945, 3422-3948, 3441-3915, 3442-3915, 3448-3915,3451-3915, 3452-3917, 3454-3674, 3454-3913, 3455-3915, 3456-3914,3456-3915, 3456-3916, 3457-3918, 3458-3922, 3459-3917, 3460-3661,3461-3915, 3463-3917, 3463-3938, 3464-3915, 3464-3916, 3465-3914,3467-3914, 3469-3919, 3472-3917, 3477-3920, 3477-3929, 3489-3917,3492-3723, 3495-3921, 3510-3935, 3511-3915, 3512-3717, 3516-3912,3519-3915, 3526-3915, 3541-3917, 3561-3783, 3566-3908, 3577-3915,3590-3808, 3600-3837, 3666-3894, 3666-3909, 3666-3919, 3713-3915,3756-3948 24/7503143CB1/ 1-680, 11-720, 22-752, 27-798, 27-824, 31-738,32-753, 32-908, 33-631, 35-665, 36-732, 37-536, 37-625, 37-695, 246037-773, 37-778, 37-804, 41-269, 41-736, 41-749, 45-586, 45-656, 55-836,59-98, 76-808, 113-625, 123-579, 123-660, 123-676, 123-682, 123-685,123-755, 123-774, 123-801, 123-825, 182-723, 182-986, 184-535, 189-525,196-658, 206-869, 231-1132, 238-959, 247-993, 247-1072, 274-828,307-865, 321-589, 326-973, 344-1076, 356-1150, 360-823, 372-687,372-931, 372-1014, 372-1048, 382-1152, 418-634, 425-1119, 426-1115,540-818, 540-981, 704-976, 823-1049, 823-1442, 856-1142, 856-1389,860-1105, 930-1138, 1009-1254, 1009-1619, 1014-1259, 1108-1249,1216-1464, 1465-1653, 1552-1851, 1558-1767, 1558-2146, 1602-1849,1604-1840, 1891-2460, 1894-2138, 1943-2450, 2025-2289, 2025-2447,2120-2391, 2123-2440, 2149-2430 25/7503563CB1/ 1-346, 1-478, 1-493,1-516, 1-518, 1-606, 1-668, 1-745, 8-244, 8-432, 10-309, 20-467, 23-408,23-489, 25-480, 25-745 745 26-436, 26-449, 26-488, 26-499, 27-370,27-668, 38-366, 59-491, 60-250, 74-389, 74-465, 74-489, 74-518, 101-387,101-402, 121-482, 163-347, 163-424, 170-424, 190-460, 242-668, 260-421,278-519, 369-515, 378-516, 518-709, 518-728, 520-742, 528-745, 555-745,563-745, 576-745, 599-745, 602-716, 673-745 26/6244251CB1/ 1-441,358-2499, 876-1149, 876-1153, 876-1269, 925-1262, 930-1552, 931-1145,933-1267, 1040-1269, 1051-1269, 2738 1248-1451, 1248-1796, 1577-1667,1881-2525, 2232-2703, 2296-2730, 2305-2730, 2417-2738 27/7503467CB1/1-110, 1-215, 1-223, 1-621, 1-623, 1-2503, 14-717, 19-370, 19-462,19-543, 19-591, 19-690, 20-688, 20-782, 63-844, 2509 94-774, 111-239,112-239, 280-718, 280-719, 280-722, 280-761, 284-930, 287-722, 301-551,313-514, 351-894, 356-598, 358-633, 369-615, 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2961-3210, 2969-3260,2970-3519, 2979-3524, 2991-3527, 2991-3569, 2995-3580, 2996-3254,3019-3223, 3019-3279, 3026-3533, 3028-3565, 3029-3526, 3031-3527,3041-3520, 3044-3284, 3057-3580, 3060-3569, 3072-3339, 3081-3314,3087-3615, 3088-3610, 3090-3525, 3104-3568, 3107-3565, 3116-3569,3120-3565, 3122-3569, 3136-3564, 3137-3571, 3139-3564, 3142-3563,3155-3568, 3174-3424, 3174-3452, 3175-3442, 3176-3373, 3181-3394,3236-3482, 3287-3577, 3325-3534, 3330-3495, 3356-3569, 3370-3592,3390-3564, 3398-3568, 3447-3569, 3456-3559 39/7505894CB1/ 1-110, 1-215,1-223, 1-621, 1-623, 1-1194, 14-717, 19-370, 19-462, 19-514, 19-543,19-636, 20-688, 20-782, 63-844, 1194 94-738, 111-239, 112-239, 280-718,280-719, 280-722, 280-761, 284-829, 287-722, 301-551, 313-514, 351-894,356-598, 358-633, 369-615, 369-658, 389-996, 407-723, 414-723, 417-609,430-622, 461-798, 473-580, 494-747, 496-747, 505-776, 510-1114,554-1194, 571-1024, 587-856, 594-841, 712-964, 712-974, 741-874,775-1053, 776-1027 40/7505901CB1/ 1-287, 3-281, 6-164, 21-276, 22-241,24-471, 27-263, 27-321, 27-334, 27-1306, 28-286, 34-220, 37-281, 37-301,37-342, 1306 39-272, 40-316, 49-221, 54-179, 54-319, 55-299, 55-333,55-336, 55-352, 56-300, 56-330, 57-266, 57-385, 57-404, 62-192, 62-221,62-307, 75-310, 76-318, 76-358, 79-471, 82-296, 86-381, 102-387,103-380, 130-374, 171-285, 177-453, 189-469, 194-430, 201-425, 202-322,204-436, 204-471, 206-453, 206-469, 206-471, 208-322, 208-471, 233-341,236-471, 237-471, 238-471, 238-500, 238-859, 278-471, 293-404, 293-416,310-390, 325-542, 446-997, 468-725, 468-729, 468-737, 468-738, 468-785,468-934, 468-951, 470-775, 471-736, 472-1056, 473-1277, 477-757,482-743, 487-699, 487-734, 498-1059, 513-1057, 515-917, 515-966,522-757, 529-794, 529-1128, 536-802, 538-1140, 544-1052, 550-754,550-756, 551-770, 554-816, 559-1065, 565-696, 584-780, 585-811, 590-884,592-839, 592-1164, 595-872, 607-873, 607-884, 609-1304, 615-785,617-1306, 620-878, 623-890, 623-894, 629-919, 629-1304, 630-1306,633-1242, 637-786, 649-908, 676-837, 676-1303, 677-1158, 677-1234,689-870, 691-1018, 701-1006, 705-979, 714-1177, 715-977, 718-874,725-1306, 729-990, 731-1276, 737-1306, 743-1009, 743-1010, 754-991,759-970, 762-1052, 781-980, 781-1140, 781-1306, 802-1013, 823-1071,825-1080, 855-1306, 857-1306, 858-1306, 871-1306, 873-1072, 873-1239,873-1306, 874-1120, 874-1306, 875-1306, 879-1306, 880-1306, 884-1128,884-1131, 886-1306, 898-1302, 904-1306, 910-1180, 912-1306, 915-1304,917-1306, 919-1306, 921-1306, 922-1306, 927-1080, 927-1306, 930-1306,937-1252, 937-1306, 941-1306, 946-1302, 952-1231, 955-1306, 956-1306,962-1306, 980-1306, 982-1231, 985-1306, 991-1306, 996-1245, 998-1252,999-1235, 1003-1259, 1003-1293, 1003-1306, 1013-1241, 1015-1287,1018-1306, 1019-1306, 1020-1306, 1028-1095, 1033-1306, 1052-1240,1064-1302, 1066-1306, 1068-1306, 1079-1306, 1087-1306, 1094-1305,1096-1306, 1104-1225, 1104-1306, 1127-1306, 1153-1306, 1190-1306,1204-1306, 1240-1306

[0410] TABLE 5 Polynucleotide Incyte Representative SEQ ID NO: ProjectID: Library 21 7500521CB1 ADMEDNV37 22 7502992CB1 COLNFET02 2371187173CB1 BRATDIC01 24 7503143CB1 BRAITUT13 25 7503563CB1 BMARTXE01 266244251CB1 TESTNOC01 27 7503467CB1 LUNGNON03 28 6599034CB1 OVARNON03 297504179CB1 PROSTUT10 30 71249354CB1 LATRTUT02 31 7505803CB1 TLYMUNT01 327505804CB1 BRSTNOT19 33 7505846CB1 EOSITXT01 34 55004585CB1 BRAUTDR04 357506012CB1 THYRNOT02 36 7506212CB1 LUNGNOT10 37 7481808CB1 TLYJTXF03 387488221CB1 THYMNOE01 39 7505894CB1 MLP000052 40 7505901CB1 LEUKNOT03

[0411] TABLE 6 Library Vector Library Description ADMEDNV37 PCR2-Library was constructed using pooled cDNA from 111 different donors.cDNA was generated using mRNA isolated from TOPOTA pooled skeletalmuscle tissue removed from 10 Caucasian male and female donors, ages21-57, who died from sudden death; from pooled thymus tissue removedfrom 9 Caucasian male and female donors, ages 18-32, who died fromsudden death; from pooled fetal liver tissue removed from 32 Caucasianmale and female fetuses, ages 18-24 weeks, who died from spontaneousabortions; from pooled fetal kidney tissue removed from 59 Caucasianmale and female fetuses, ages 20-33 weeks, who died from spontaneousabortions; and from fetal brain tissue removed from a 23-week-oldCaucasian male fetus who died from fetal demise. BMARTXE01 pINCY This 5′biased random primed library was constructed using RNA isolated fromtreated SH-SY5Y cells derived from a metastatic bone marrowneuroblastoma, removed from a 4-year-old Caucasian female (Schering AG).The medium was MEM/HAM'S F12 with 10% fetal calf serum. After reachingabout 80% confluency cells were treated with 6- Hydroxydopamine (6-OHDA)at 100 microM for 8 hours. BRAITUT13 pINCY Library was constructed usingRNA isolated from brain tumor tissue removed from the left frontal lobeof a 68-year-old Caucasian male during excision of a cerebral meningeallesion. Pathology indicated a meningioma in the left frontal lobe.BRATDIC01 pINCY This large size-fractionated library was constructedusing RNA isolated from diseased brain tissue removed from the lefttemporal lobe of a 27-year-old Caucasian male during a brain lobectomy.Pathology for the left temporal lobe, including the mesial temporalstructures, indicated focal, marked pyramidal cell loss and gliosis inhippocampal sector CA1, consistent with mesial temporal sclerosis. Theleft frontal lobe showed a focal deep white matter lesion, characterizedby marked gliosis, calcifications, and hemosiderin-laden macrophages,consistent with a remote perinatal injury. The frontal lobe tissue alsoshowed mild to moderate generalized gliosis, predominantly subpial andsubcortical, consistent with chronic seizure disorder. GFAP was positivefor astrocytes. The patient presented with intractable epilepsy, focalepilepsy, hemiplegia, and an unspecified brain injury. Patient historyincluded cerebral palsy, abnormality of gait, depressive disorder, andtobacco abuse in remission. Previous surgeries included tendon transfer.Patient medications included minocycline hydrochloride, Tegretol,phenobarbital, vitamin C, Pepcid, and Pevaryl. Family history includedbrain cancer in the father. BRAUTDR04 PCDNA2.1 This random primedlibrary was constructed using RNA isolated from pooled striatum, dorsalcaudate nucleus, dorsal putamen, and ventral nucleus accumbens tissueremoved from a 55-year-old Caucasian female who died fromcholangiocarcinoma. Pathology indicated mild meningeal fibrosispredominately over the convexities, scattered axonal spheroids in thewhite matter of the cingulate cortex and the thalamus, and a fewscattered neurofibrillary tangles in the entorhinal cortex and theperiaqueductal gray region. Pathology for the associated tumor tissueindicated well-differentiated cholangiocarcinoma of the liver withresidual or relapsed tumor. Patient history included cholangiocarcinoma,post-operative Budd-Chiari syndrome, biliary ascites, hydrothorax,dehydration, malnutrition, oliguria and acute renal failure. Previoussurgeries included cholecystectomy and resection of 85% of the liver.BRSTNOT19 pINCY Library was constructed using RNA isolated from breasttissue removed from a 67-year-old Caucasian female during a unilateralextended simple mastectomy. Pathology for the associated tumor tissueindicated residual invasive lobular carcinoma. Patient history includeddepressive disorder, benign large bowel neoplasm, and hemorrhoids.Family history included cerebrovascular and cardiovascular disease andlung cancer. COLNFET02 pINCY Library was constructed using RNA isolatedfrom the colon tissue of a Caucasian female fetus, who died at 20 weeks'gestation. EOSITXT01 pINCY Library was constructed using RNA isolatedfrom eosinophils stimulated with IL-5. LATRTUT02 pINCY Library wasconstructed using RNA isolated from a myxoma removed from the leftatrium of a 43-year-old Caucasian male during annuloplasty. Pathologyindicated atrial myxoma. Patient history included pulmonaryinsufficiency, acute myocardial infarction, atherosclerotic coronaryartery disease, hyperlipidemia, and tobacco use. Family history includedbenign hypertension, acute myocardial infarction, atheroscleroticcoronary artery disease, and type II diabetes. LEUKNOT03 pINCY Librarywas constructed using RNA isolated from white blood cells of a27-year-old female with blood type A+. The donor tested negative forcytomegalovirus (CMV). LUNGNON03 PSPORT1 This normalized library wasconstructed from 2.56 million independent clones from a lung tissuelibrary. RNA was made from lung tissue removed from the left lobe of a58-year-old Caucasian male during a segmental lung resection. Pathologyfor the associated tumor tissue indicated a metastatic grade 3 (of 4)osteosarcoma. Patient history included soft tissue cancer, secondarycancer of the lung, prostate cancer, and an acute duodenal ulcer withhemorrhage. Patient also received radiation therapy to theretroperitoneum. Family history included prostate cancer, breast cancer,and acute leukemia. The normalization and hybridization conditions wereadapted from Soares et al., PNAS (1994) 91: 9228; Swaroop et al., NAR(1991) 19: 1954; and Bonaldo et al., Genome Research (1996) 6: 791.LUNGNOT10 pINCY Library was constructed using RNA isolated from the lungtissue of a Caucasian male fetus, who died at 23 weeks' gestation.MLP000052 PCR2- Library was constructed using pooled cDNA from differentdonors. cDNA was generated using mRNA isolated from the TOPOTAfollowing: aorta, cerebellum, lymph nodes, muscle, tonsil (lymphoidhyperplasia), bladder tumor (invasive grade 3 transitional cellcarcinoma.), breast (proliferative fibrocystic changes without atypiacharacterized by epithelial ductal hyperplasia, testicle tumor(embryonal carcinoma), spleen, ovary, parathyroid, ileum, breast skin,sigmoid colon, penis tumor (fungating invasive grade 4 squamous cellcarcinoma), fetal lung,, breast, fetal small intestine, fetal liver,fetal pancreas, fetal lung, fetal skin, fetal penis, fetal bone, fetalribs, frontal brain tumor (grade 4 gemistocytic astrocytoma), ovary(stromal hyperthecosis), bladder, bladder tumor (invasive grade 3transitional cell carcinoma), stomach, lymph node tumor (metastaticbasaloid squamous cell carcinoma), tonsil (reactive lymphoidhyperplasia), periosteum from the tibia, fetal brain, fetal spleen,uterus tumor, endometrial (grade 3 adenosquamous carcinoma), seminalvesicle, liver, aorta, adrenal gland, lymph node (metastatic grade 3squamous cell carcinoma), glossal muscle, esophagus, esophagus tumor(invasive grade 3 adenocarcinoma), ileum, pancreas, soft tissue tumorfrom the skull (grade 3 ependymoma), transverse colon, (benign familialpolyposis), rectum tumor (grade 3 colonic adenocarcinoma), rib tumor,(metastatic grade 3 osteosarcoma), lung, heart, placenta, thymus,stomach, spleen (splenomegaly with congestion), uterus, cervix (mildchronic cervicitis with focal squamous metaplasia), spleen tumor(malignant lymphoma, diffuse large cell type, B-cell phenotype withabundant reactive T-cells and marked granulomatous response), umbilicalcord blood mononuclear cells, upper lobe lung tumor, (grade 3 squamouscell carcinoma), endometrium (secretory phase), liver, liver tumor(metastatic grade 2 neuroendocrine carcinoma), colon, umbilical cordblood, Th1 cells, nonactivated, umbilical cord blood, Th2 cells,nonactivated, coronary artery endothelial cells (untreated), coronaryartery smooth muscle cells, (untreated), coronary artery smooth musclecells (treated with TNF & IL-1 10 ng/ml each for 20 hours), bladder(mild chronic cystitis), epiglottis, breast skin, small intestine, fetalprostate stroma fibroblasts, prostate epithelial cells (PrEC cells),fetal adrenal glands, fetal liver, kidney transformed embryonal cellline (293-EBNA) (untreated), kidney transformed embryonal cell line(293-EBNA) (treated with 5Aza-2deoxycytidine for 72 hours), mammaryepithelial cells, (HMEC cells), peripheral blood monocytes (treated withIL-10 at time 0, 10 ng/ml, LPS was added at 1 hour at 5 ng/ml.Incubation 24 hours), peripheral blood monocytes (treated withanti-IL-10 at time 0, 10 ng/ml, LPS was added at 1 hour at 5 ng/ml.Incubation 24 hours), spinal cord, base of medulla (Huntington'schorea), thigh and arm muscle (ALS), breast skin fibroblast (untreated),breast skin fibroblast (treated with 9CIS Retinoic Acid 1 μM for 20hours), breast skin fibroblast (treated with TNF-alpha & IL-1 beta, 10ng/ml each for 20 hours), fetal liver mast cells, hematopoietic (Mastcells prepared from human fetal liver hematopoietic progenitor cells(CD34+ stem cells) cultured in the presence of hIL-6 and hSCF for 18days), epithelial layer of colon, bronchial epithelial cells (treatedfor 20 hours with 20% smoke conditioned media), lymph node, pooledperipheral blood mononuclear cells (untreated), pooled brain segments:striatum, globus pallidus and posterior putamen (Alzheimer's Disease),pituitary gland, umbilical cord blood, CD34+ derived dendritic cells(treated with SCF, GM-CSF & TNF alpha, 13 days), umbilical cord blood,CD34+ derived dendritic cells (treated with SCF, GM-CSF & TNF alpha, 13days followed by PMA/Ionomycin for 5 hours), small intestine, rectum,bone marrow neuroblastoma cell line (SH-SY5Y cells, treated with6-Hydroxydopamine 100 uM for 8 hours), bone marrow, neuroblastoma cellline (SH-SY5Y cells, untreated), brain segments from one donor:amygdala, entorhinal cortex, globus pallidus, substantia innominata,striatum, dorsal caudate nucleus, dorsal putamen, ventral nucleusaccumbens, archaecortex (hippocampus anterior and posterior), thalamus,nucleus raphe magnus, periaqueductal gray, midbrain, substantia nigra,and dentate nucleus, pineal gland (Alzheimer's Disease), preadipocytes(untreated), preadipocytes (treated with a peroxisomeproliferator-activated receptor gamma agonist, 1microM, 4 hours), pooledprostate (adenofibromatous hyperplasia), pooled kidney, pooledadipocytes (untreated), pooled adipocytes (treated with human insulin),pooled mesentaric and abdomenal fat, pooled adrenal glands, pooledthyroid (normal and adenomatous hyperplasia), pooled spleen (normal andwith changes consistent with idiopathic thrombocytopenic purpura),pooled right and left breast pooled lung, pooled nasal polyps, pooledfat, pooled synovium (normal and rhumatoid arthritis), pooled brain(meningioma, gemistocytic astrocytoma. and Alzheimer's disease), pooledfetal colon, pooled colon: ascending, descending (chronic ulcerativecolitis), and rectal tumor (adenocarcinoma), pooled esophagus, normaland tumor (invasive grade 3 adenocarcinoma), pooled breast skinfibroblast (one treated w/9CIS Retinoic Acid and the other withTNF-alpha & IL-1 beta), pooled gallbladder (acute necrotizingcholecystitis with cholelithiasis (clinically hydrops), acutehemorrhagic cholecystitis with cholelithiasis, chronic cholecystitis andcholelithiasis), pooled fetal heart, (Patau's and fetal demise), pooledneurogenic tumor cell line, SK-N-MC, (neuroepitelioma, metastasis tosupra-orbital area, untreated) and neuron, NT-2 cell line, (treated withmouse leptin at 1 μg/ml and 9cis retinoic acid at 3.3 μM for 6 days),pooled ovary (normal and polycystic ovarian disease), pooled prostate,(adenofibromatous hyperplasia), pooled seminal vesicle, pooled smallintestine, pooled fetal small intestine, pooled stomach and fetalstomach, prostate epithelial cells, pooled testis (normal and embryonalcarcinoma), pooled uterus, pooled uterus tumor (grade 3 adenosquamouscarcinoma and leiomyoma), pooled uterus, endometrium, and myometrium,(normal and adenomatous hyperplasia with squamous metaplasia and focalatypia), pooled brain: (temporal lobe meningioma, cerebellum andhippocampus (Alzheimer's Disease), pooled skin, fetal lung, adrenaltumor (adrenal cortical carcinoma), prostate tumor (adenocarcinoma),fetal heart, fetal small intestine, ovary tumor (mucinous cystadenoma),ovary, ovary tumor (transitional cell carcinoma), disease prostate(adenofibromatous hyperplasia), fetal colon, uterus tumor (leiomyoma),temporal brain, submandibular gland, colon tumor (adenocarcinoma),ascending and transverse colon, ovary tumor (endometrioid carcinoma),lung tumor (squamous cell carcinoma), fetal brain, fetal lung, uretertumor (transitional cell carcinoma), untreated HNT cells, para-aorticsoft tissue, testis, seminal vesicle, diseased ovary (endometriosis),temporal lobe, myometrium, diseased gallbladder (cholecystitis,cholelithiasis), placenta, breast tumor (ductal adenocarcinoma), breast,lung tumor (liposarcoma), endometrium, abdominal fat, cervical spinedorsal root ganglion, thoracic spine dorsal root ganglion, diseasedthyroid (adenomatous hyperplasia), liver, kidney, fetal liver, NT-2cells (treated with mouse leptin and 9cis RA), K562 cells (treated with9cis RA), cerebellum, corpus callosum, hypothalamus, fetal brainastrocytes (treated with TNFa and IL-1b), inferior parietal cortex,posterior hippocampus, pons, thalamus, C3A cells (untreated), C3A cells(treated with 3-methylcholanthrene), testis, colon epithelial layer,pooled prostate, pooled liver, substantia nigra, thigh muscle, rib bone,fallopian tube tumor (endometrioid and serous adenocarcinoma), diseasedlung (idiopathic pulmonary disease), cingulate anterior allocortex andneocortex, cingulate posterior allocortex, auditory neocortex, frontalneocortex, orbital inferior neocortex, parietal superior neocortex,visual primary neocortex, dentate nucleus, posterior cingulate,cerebellum, vermis, inferior temporal cortex, medulla, posteriorparietal cortex, colon polyp, pooled breast, anterior and posteriorhippocampus, mesenteric and abdominal fat, pooled esophagus, pooledfetal kidney, pooled fetal liver, ileum, small intestine, pooledgallbladder, frontal and superior temporal cortex, pooled ovary, pooledendometrium, pooled prostate, pooled kidney, fetal femur, sacrum tumor(giant cell tumor), pooled kidney and kidney tumor (renal cell carcinomaclear-cell type), pooled liver and liver tumor (neuroendocrinecarcinoma), pooled fetal liver, pooled lung, fetal pancreas, pancreas,parotid gland, parotid tumor (sebaceous lymphadenoma), retroperitonealand suprglottic soft tissue, spleen, fetal spleen, spleen tumor(malignant lymphoma), diseased spleen (idiopathic thrombocytopenicpurpura), parathyroid, thyroid, thymus, tonsil ureter tumor(transitional cell carcinoma), pooled adrenal gland and adrenal tumor(pheochromocytoma), pooled lymph node tumor (Hodgkin's disease andmetastatic adenocarcinoma), pooled neck and calf muscles, and pooledbladder. OVARNON03 pINCY This normalized ovarian tissue library wasconstructed from 5 million independent clones from an ovary library.Starting RNA was made from ovarian tissue removed from a 36-year-oldCaucasian female during total abdominal hysterectomy, bilateralsalpingo-oophorectomy, soft tissue excision, and an incidentalappendectomy. Pathology for the associated tumor tissue indicated oneintramural and one subserosal leiomyomata of the myometrium. Theendometrium was proliferative phase. Patient history included deficiencyanemia, calculus of the kidney, and a kidney anomaly. Family historyincluded hyperlipidemia, acute myocardial infarction, atheroscleroticcoronary artery disease, type II diabetes, and chronic liver disease.The library was normalized in two rounds using conditions adapted fromSoares et al., PNAS (1994) 91: 9228 and Bonaldo et al., Genome Research(1996) 6: 791, except that a significantly longer (48 hours/round)reannealing hybridization was used. PROSTUT10 pINCY Library wasconstructed using RNA isolated from prostatic tumor tissue removed froma 66-year-old Caucasian male during radical prostatectomy and regionallymph node excision. Pathology indicated an adenocarcinoma (Gleasongrade 2 + 3). Adenofibromatous hyperplasia was also present. The patientpresented with elevated prostate specific antigen (PSA). Family historyincluded prostate cancer and secondary bone cancer. TESTNOC01 PBLUE-This large size fractionated library was constructed using RNA isolatedfrom testicular tissue removed from a pool of SCRIPT eleven, 10 to61-year-old Caucasian males. THYMNOE01 PCDNA2.1 This 5′ biased randomprimed library was constructed using RNA isolated from thymus tissueremoved from a 2-year-old Caucasian female during a thymectomy and patchclosure of left atrioventricular fistula. Pathology indicated there wasno gross abnormality of the thymus. The patient presented withcongenital heart abnormalities. Patient history included double inletleft ventricle and a rudimentary right ventricle, pulmonaryhypertension, cyanosis, subaortic stenosis, seizures, and a fracture ofthe skull base. Patient medications included Lasix and Captopril. Familyhistory included reflux neuropathy in the mother. THYRNOT02 PSPORT1Library was constructed using RNA isolated from the diseased thyroidtissue of a 16-year-old Caucasian female with Graves' disease(hyperthyroidism). TLYJTXF03 pRARE This 5′ cap isolated full-lengthlibrary was constructed using RNA isolated from a treated Jurkat cellline derived from the T cells of a male. The cells were treated with 10ng/mL of anti-CD3 for 5 minutes. The cells were then fractionated toobtain the nuclei. Patient history included acute T-cell leukemia.TLYMUNT01 pINCY Library was constructed using RNA isolated from restingallogenic T-lymphocyte tissue removed from an adult (40-50-year old)Caucasian male.

[0412] TABLE 7 Parameter Program Description Reference Threshold ABI Aprogram that removes vector sequences and Applied Biosystems, FosterCity, CA. FACTURA masks ambiguous bases in nucleic acid sequences. ABI/A Fast Data Finder useful in comparing and Applied Biosystems, FosterCity, CA; Mismatch PARACEL annotating amino acid or nucleic acidsequences. Paracel Inc., Pasadena, CA. <50% FDF ABI A program thatassembles nucleic acid sequences. Applied Biosystems, Foster City, CA.AutoAssembler BLAST A Basic Local Alignment Search Tool useful inAltschul, S. F. et al. (1990) J. Mol. Biol. ESTs: sequence similaritysearch for amino acid and 215: 403-410; Altschul, S. F. et al. (1997)Probability nucleic acid sequences. BLAST includes five Nucleic AcidsRes. 25: 3389-3402. value = 1.0E−8 functions: blastp, blastn, blastx,tblastn, and tblastx. or less; Full Length sequences: Probability value= 1.0E−10 or less FASTA A Pearson and Lipman algorithm that searches forPearson, W. R. and D. J. Lipman (1988) Proc. ESTs: fasta E similaritybetween a query sequence and a group of Natl. Acad Sci. USA 85:2444-2448; Pearson, value = sequences of the same type. FASTA comprisesas W. R. (1990) Methods Enzymol. 183: 63-98; 1.06E−6; least fivefunctions: fasta, tfasta, fastx, tfastx, and and Smith, T. F. and M. S.Waterman (1981) Assembled ssearch. Adv. Appl. Math. 2: 482-489. ESTs:fasta Identity = 95% or greater and Match length = 200 bases or greater;fastx E value = 1.0E−8 or less; Full Length sequences: fastx score = 100or greater BLIMPS A BLocks IMProved Searcher that matches a Henikoff, S.and J. G. Henikoff (1991) Nucleic Probability sequence against those inBLOCKS, PRINTS, Acids Res. 19: 6565-6572; Henikoff, J. G. and value =1.0E−3 DOMO, PRODOM, and PFAM databases to search S. Henikoff (1996)Methods Enzymol. or less for gene families, sequence homology, andstructural 266: 88-105; and Attwood, T. K. et al. (1997) J. fingerprintregions. Chem. Inf. Comput. Sci. 37: 417-424. HMMER An algorithm forsearching a query sequence against Krogh, A. et al. (1994) J. Mol. Biol.PFAM, INCY, hidden Markov model (HMM)-based databases of 235: 1501-1531;Sonnhammer, E. L. L. et al. SMART or protein family consensus sequences,such as PFAM, (1988) Nucleic Acids Res. 26: 320-322; TIGRFAM INCY, SMARTand TIGRFAM. Durbin, R. et al. (1998) Our World View, in a hits:Nutshell, Cambridge Univ. Press, pp. 1-350. Probability value = 1.0E−3or less; Signal peptide hits: Score = 0 or greater ProfileScan Analgorithm that searches for structural and sequence Gribskov, M. et al.(1988) CABIOS 4: 61-66; Normalized motifs in protein sequences thatmatch sequence patterns Gribskov, M. et al. (1989) Methods Enzymol.quality score ≧ defined in Prosite. 183: 146-159; Bairoch, A. et al.(1997) GCG-specified Nucleic Acids Res. 25: 217-221. “HIGH” value forthat particular Prosite motif. Generally, score = 1.4-2.1. Phred Abase-calling algorithm that examines automated Ewing, B. et al. (1998)Genome Res. sequencer traces with high sensitivity and probability. 8:175-185; Ewing, B. and P. Green (1998) Genome Res. 8: 186-194. Phrap APhils Revised Assembly Program including SWAT and Smith, T. F. and M. S.Waterman (1981) Adv. Score = 120 or CrossMatch, programs based onefficient implementation Appl. Math. 2: 482-489; Smith, T. F. and M. S.greater; of the Smith-Waterman algorithm, useful in searching Waterman(1981) J. Mol. Biol. 147: 195-197; Match length = sequence homology andassembling DNA sequences. and Green, P., University of Washington, 56 orgreater Seattle, WA. Consed A graphical tool for viewing and editingPhrap assemblies. Gordon, D. et al. (1998) Genome Res. 8: 195-202.SPScan A weight matrix analysis program that scans protein Nielson, H.et al. (1997) Protein Engineering Score = 3.5 or sequences for thepresence of secretory signal peptides. 10: 1-6; Claverie, J. M. and S.Audic (1997) greater CABIOS 12: 431-439. TMAP A program that uses weightmatrices to delineate Persson, B. and P. Argos (1994) J. Mol. Biol.transmembrane segments on protein sequences and 237: 182-192; Persson,B. and P. Argos (1996) determine orientation. Protein Sci. 5: 363-371.TMHMMER A program that uses a hidden Markov model (HMM) to Sonnhammer,E. L. et al. (1998) Proc. Sixth Intl. delineate transmembrane segmentson protein sequences Conf. On Intelligent Systems for Mol. Biol., anddetermine orientation. Glasgow et al., eds., The Am. Assoc. forArtificial Intelligence (AAAI) Press, Menlo Park, CA, and MIT Press,Cambridge, MA pp. 175-182. Motifs A program that searches amino acidsequences for patterns Bairoch, A. et al. (1997) Nucleic Acids thatmatched those defined in Prosite. Res. 25: 217-221; Wisconsin PackageProgram Manual, version 9, page M51-59, Genetics Computer Group,Madison, WI.

[0413] TABLE 8 Cau- casian African Asian Hispanic SEQ Allele 1 Allele 1Allele 1 Allele 1 ID EST CB1 EST Allele Allele Amino fre- fre- fre- fre-NO: PID EST ID SNP ID SNP SNP Allele 1 2 Acid quency quency quencyquency 36 7506212 1334172H1 SNP00001710 124 174 C G C A40 n/a n/a n/an/a 36 7506212 1342069H1 SNP00015140 344 563 C C G non- n/a n/a n/a n/acoding 36 7506212 1342069H1 SNP00015141 82 4611 A A C non- 0.92 n/a n/an/a coding 36 7506212 1376878H1 SNP00019042 201 4198 T T C non- n/d n/an/a n/a coding 36 7506212 1413622H1 SNP00146236 65 4948 G G C non- n/an/a n/a n/a coding 36 7506212 1990335H1 SNP00003545 89 3544 A G A V11630.33 0.30 0.37 0.49 36 7506212 2097343H1 SNP00023386 82 3287 G G A E1078n/a n/a n/a n/a 36 7506212 2444202H1 SNP00112338 213 2084 G G C G677 n/dn/d n/d n/d 36 7506212 3373271H1 SNP00019041 88 4015 T T C non- n/a n/an/a n/a coding 36 7506212 5029814H1 SNP00063493 38 1719 A A G T222 0.89n/a n/a n/a 38 7488221 1287507H1 SNP00143006 216 580 A A C K187 n/a n/an/a n/a 38 7488221 1643522H1 SNP00000508 71 2704 C C A non- 0.87 0.790.93 0.76 coding 38 7488221 3487206H1 SNP00000508 42 2702 A C A non-0.87 0.79 0.93 0.76 coding 38 7488221 3973154H1 SNP00000508 35 2703 C CA non- 0.87 0.79 0.93 0.76 coding 38 7488221 5290303H1 SNP00000509 1233373 T T C non- n/a n/a n/a n/a coding 38 7488221 5464541H1 SNP0014300695 579 A A C K187 n/a n/a n/a n/a 38 7488221 5796955H1 SNP00000509 4403375 T T C non- n/a n/a n/a n/a coding 38 7488221 6205687H1 SNP0013251563 1163 C T C H382 n/a n/a n/a n/a 39 7505894 2688406H1 SNP00061373 113841 T T C non- n/a n/a n/a n/a coding 39 7505894 5802504H1 SNP0006137360 832 T T C non- n/a n/a n/a n/a coding 40 7505901 1723825H1SNP00041209 111 983 G G C K236 n/a n/a n/a n/a 40 7505901 405880H1SNP00041209 100 984 G G C E237 n/a n/a n/a n/a 40 7505901 4435683H1SNP00041209 239 982 G G C R236 n/a n/a n/a n/a 40 7505901 6870884H1SNP00041209 236 986 G G C K237 n/a n/a n/a n/a

[0414]

0 SEQUENCE LISTING <160> NUMBER OF SEQ ID NOS: 40 <210> SEQ ID NO 1<211> LENGTH: 380 <212> TYPE: PRT <213> ORGANISM: Homo sapiens <220>FEATURE: <221> NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte IDNo: 7500521CD1 <400> SEQUENCE: 1 Met Val Gly Phe Gly Ala Asn Arg Arg AlaGly Arg Leu Pro Ser 1 5 10 15 Leu Val Leu Val Val Leu Leu Val Val IleVal Val Leu Ala Phe 20 25 30 Asn Tyr Trp Ser Ile Ser Ser Arg His Val LeuLeu Gln Glu Glu 35 40 45 Val Ala Glu Leu Gln Gly Gln Val Gln Arg Thr GluVal Ala Arg 50 55 60 Gly Arg Leu Glu Lys Arg Asn Ser Asp Leu Leu Leu LeuVal Asp 65 70 75 Thr His Lys Lys Gln Ile Asp Gln Lys Glu Ala Asp Tyr GlyArg 80 85 90 Leu Ser Ser Arg Leu Gln Ala Arg Glu Gly Leu Gly Lys Arg Cys95 100 105 Glu Asp Asp Lys Val Lys Leu Gln Asn Asn Ile Ser Tyr Gln Met110 115 120 Ala Asp Ile His His Leu Lys Glu Gln Leu Ala Glu Leu Arg Gln125 130 135 Glu Phe Leu Arg Gln Glu Asp Gln Leu Gln Asp Tyr Arg Lys Asn140 145 150 Asn Thr Tyr Leu Val Lys Arg Leu Glu Tyr Glu Ser Phe Gln Cys155 160 165 Gly Gln Gln Met Lys Glu Leu Arg Ala Gln His Glu Glu Asn Ile170 175 180 Lys Lys Leu Ala Asp Gln Phe Leu Glu Glu Gln Lys Gln Glu Thr185 190 195 Gln Lys Ile Gln Ser Asn Asp Gly Lys Glu Leu Asp Ile Asn Asn200 205 210 Gln Val Val Pro Lys Asn Ile Pro Lys Val Ala Glu Asn Val Ala215 220 225 Asp Lys Asn Glu Glu Pro Ser Ser Asn His Ile Pro His Gly Lys230 235 240 Glu Gln Ile Lys Arg Gly Gly Asp Ala Gly Met Pro Gly Ile Glu245 250 255 Glu Asn Asp Leu Ala Lys Val Asp Asp Leu Pro Pro Ala Leu Arg260 265 270 Lys Pro Pro Ile Ser Val Ser Gln His Glu Ser His Gln Ala Ile275 280 285 Ser His Leu Pro Thr Gly Gln Pro Leu Ser Pro Asn Met Pro Pro290 295 300 Asp Ser His Ile Asn His Asn Gly Asn Pro Gly Thr Ser Lys Gln305 310 315 Asn Pro Ser Ser Pro Leu Gln Arg Leu Ile Pro Gly Ser Asn Leu320 325 330 Asp Ser Glu Pro Arg Ile Gln Thr Asp Ile Leu Lys Gln Ala Thr335 340 345 Lys Asp Arg Val Ser Asp Phe His Lys Leu Lys Gln Asn Asp Glu350 355 360 Glu Arg Glu Leu Gln Met Asp Pro Ala Asp Tyr Gly Lys Gln His365 370 375 Phe Asn Asp Val Leu 380 <210> SEQ ID NO 2 <211> LENGTH: 326<212> TYPE: PRT <213> ORGANISM: Homo sapiens <220> FEATURE: <221>NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte ID No: 7502992CD1<400> SEQUENCE: 2 Met Ala His Cys Cys Leu Gly Gly Leu Ala Glu Phe LeuGln Ser 1 5 10 15 Phe Gln Gln Arg Val Glu Arg Phe His Glu Asn Pro AlaVal Arg 20 25 30 Glu Met Leu Pro Asp Thr Tyr Ile Ser Lys Thr Ile Ala LeuVal 35 40 45 Asn Cys Gly Pro Pro Leu Arg Ala Leu Ala Glu Arg Leu Ala Arg50 55 60 Val Gly Pro Pro Glu Ser Glu Pro Ala Arg Glu Ala Ser Ala Ser 6570 75 Ala Leu Asp His Val Thr Arg Leu Cys His Arg Val Val Ala Asn 80 8590 Leu Leu Phe Gln Glu Leu Gln Pro His Phe Asn Lys Leu Met Arg 95 100105 Arg Lys Trp Leu Ser Ser Pro Glu Ala Leu Asp Gly Ile Val Gly 110 115120 Thr Leu Gly Ala Gln Ala Leu Ala Leu Arg Arg Met Gln Asp Glu 125 130135 Pro Tyr Gln Ala Leu Val Ala Glu Leu His Arg Arg Ala Leu Val 140 145150 Glu Tyr Val Arg Pro Leu Leu Arg Gly Arg Leu Arg Cys Ser Ser 155 160165 Ala Arg Thr Arg Ser Arg Val Ala Gly Arg Leu Arg Glu Asp Ala 170 175180 Ala Gln Leu Gln Arg Leu Phe Arg Arg Leu Glu Ser Gln Ala Ser 185 190195 Trp Leu Asp Ala Val Val Pro His Leu Ala Glu Val Met Gln Leu 200 205210 Glu Asp Thr Pro Ser Ile Gln Val Glu Val Gly Val Leu Val Arg 215 220225 Asp Tyr Pro Asp Ile Arg Gln Lys His Val Ala Ala Leu Leu Asp 230 235240 Ile Arg Gly Leu Arg Asn Thr Ala Ala Arg Gln Glu Ile Leu Ala 245 250255 Val Ala Arg Asp Leu Glu Leu Ser Glu Glu Gly Ala Leu Ser Pro 260 265270 Pro Arg Asp Arg Ala Phe Phe Ala Asp Ile Pro Val Pro Arg Pro 275 280285 Ser Phe Cys Leu Ser Leu Pro Leu Phe Leu Gly Arg Leu Pro Leu 290 295300 Ser Arg Leu Ala Arg Pro Ser Leu Ala Cys Leu Pro Arg Pro Arg 305 310315 Pro Pro Ser Leu Ala Arg Pro Arg Ala Gln Arg 320 325 <210> SEQ ID NO3 <211> LENGTH: 744 <212> TYPE: PRT <213> ORGANISM: Homo sapiens <220>FEATURE: <221> NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte IDNo: 71187173CD1 <400> SEQUENCE: 3 Met Ala Gly Arg Ser Met Gln Ala AlaArg Cys Pro Thr Asp Glu 1 5 10 15 Leu Ser Leu Thr Asn Cys Ala Val ValAsn Glu Lys Asp Phe Gln 20 25 30 Ser Gly Gln His Val Ile Val Arg Thr SerPro Asn His Arg Tyr 35 40 45 Thr Phe Thr Leu Lys Thr His Pro Ser Val ValPro Gly Ser Ile 50 55 60 Ala Phe Ser Leu Pro Gln Arg Lys Trp Ala Gly LeuSer Ile Gly 65 70 75 Gln Glu Ile Glu Val Ser Leu Tyr Thr Phe Asp Lys AlaLys Gln 80 85 90 Cys Ile Gly Thr Met Thr Ile Glu Ile Asp Phe Leu Gln LysLys 95 100 105 Ser Ile Asp Ser Asn Pro Tyr Asp Thr Asp Lys Met Ala AlaGlu 110 115 120 Phe Ile Gln Gln Phe Asn Asn Gln Ala Phe Ser Val Gly GlnGln 125 130 135 Leu Val Phe Ser Phe Asn Glu Lys Leu Phe Gly Leu Leu ValLys 140 145 150 Asp Ile Glu Ala Met Asp Pro Ser Ile Leu Lys Gly Glu ProAla 155 160 165 Thr Gly Lys Arg Gln Lys Ile Glu Val Gly Leu Val Val GlyAsn 170 175 180 Ser Gln Val Ala Phe Glu Lys Ala Glu Asn Ser Ser Leu AsnLeu 185 190 195 Ile Gly Lys Ala Lys Thr Lys Glu Asn Arg Gln Ser Ile IleAsn 200 205 210 Pro Asp Trp Asn Phe Glu Lys Met Gly Ile Gly Gly Leu AspLys 215 220 225 Glu Phe Ser Asp Ile Phe Arg Arg Ala Phe Ala Ser Arg ValPhe 230 235 240 Pro Pro Glu Ile Val Glu Gln Met Gly Cys Lys His Val LysGly 245 250 255 Ile Leu Leu Tyr Gly Pro Pro Gly Cys Gly Lys Thr Leu LeuAla 260 265 270 Arg Gln Ile Gly Lys Met Leu Asn Ala Arg Glu Pro Lys ValVal 275 280 285 Asn Gly Pro Glu Ile Leu Asn Lys Tyr Val Gly Glu Ser GluAla 290 295 300 Asn Ile Arg Lys Leu Phe Ala Asp Ala Glu Glu Glu Gln ArgArg 305 310 315 Leu Gly Ala Asn Ser Gly Leu His Ile Ile Ile Phe Asp GluIle 320 325 330 Asp Ala Ile Cys Lys Gln Arg Gly Ser Met Ala Gly Ser ThrGly 335 340 345 Val His Asp Thr Val Val Asn Gln Leu Leu Ser Lys Ile AspGly 350 355 360 Val Glu Gln Leu Asn Asn Ile Leu Val Ile Gly Met Thr AsnArg 365 370 375 Pro Asp Leu Ile Asp Glu Ala Leu Leu Arg Pro Gly Arg LeuGlu 380 385 390 Val Lys Met Glu Ile Gly Leu Pro Asp Glu Lys Gly Arg LeuGln 395 400 405 Ile Leu His Ile His Thr Ala Arg Met Arg Gly His Gln LeuLeu 410 415 420 Ser Ala Asp Val Asp Ile Lys Glu Leu Ala Val Glu Thr LysAsn 425 430 435 Phe Ser Gly Ala Glu Leu Glu Gly Leu Val Arg Ala Ala GlnSer 440 445 450 Thr Ala Met Asn Arg His Ile Lys Ala Ser Thr Lys Val GluVal 455 460 465 Asp Met Glu Lys Ala Glu Ser Leu Gln Val Thr Arg Gly AspPhe 470 475 480 Leu Ala Ser Leu Glu Asn Asp Ile Lys Pro Ala Phe Gly ThrAsn 485 490 495 Gln Glu Asp Tyr Ala Ser Tyr Ile Met Asn Gly Ile Ile LysTrp 500 505 510 Gly Asp Pro Val Thr Arg Val Leu Asp Asp Gly Glu Leu LeuVal 515 520 525 Gln Gln Thr Lys Asn Ser Asp Arg Thr Pro Leu Val Ser ValLeu 530 535 540 Leu Glu Gly Pro Pro His Ser Gly Lys Thr Ala Leu Ala AlaLys 545 550 555 Ile Ala Glu Glu Ser Asn Phe Pro Phe Ile Lys Ile Cys SerPro 560 565 570 Asp Lys Met Ile Gly Phe Ser Glu Thr Ala Lys Cys Gln AlaMet 575 580 585 Lys Lys Ile Phe Asp Asp Ala Tyr Lys Ser Gln Leu Ser CysVal 590 595 600 Val Val Asp Asp Ile Glu Arg Leu Leu Asp Tyr Val Pro IleGly 605 610 615 Pro Arg Phe Ser Asn Leu Val Leu Gln Ala Leu Leu Val LeuLeu 620 625 630 Lys Lys Ala Pro Pro Gln Gly Arg Lys Leu Leu Ile Ile GlyThr 635 640 645 Thr Ser Arg Lys Asp Val Leu Gln Glu Met Glu Met Leu AsnAla 650 655 660 Phe Ser Thr Thr Ile His Val Pro Asn Ile Ala Thr Gly GluGln 665 670 675 Leu Leu Glu Ala Leu Glu Leu Leu Gly Asn Phe Lys Asp LysGlu 680 685 690 Arg Thr Thr Ile Ala Gln Gln Val Lys Gly Lys Lys Val TrpIle 695 700 705 Gly Ile Lys Lys Leu Leu Met Leu Ile Glu Met Ser Leu GlnMet 710 715 720 Asp Pro Glu Tyr Arg Val Arg Lys Phe Leu Ala Leu Leu ArgGlu 725 730 735 Glu Gly Ala Ser Pro Leu Asp Phe Asp 740 <210> SEQ ID NO4 <211> LENGTH: 648 <212> TYPE: PRT <213> ORGANISM: Homo sapiens <220>FEATURE: <221> NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte IDNo: 7503143CD1 <400> SEQUENCE: 4 Met Ser Trp Leu Phe Gly Ile Asn Lys GlyPro Lys Gly Glu Gly 1 5 10 15 Ala Gly Pro Pro Pro Pro Leu Pro Pro AlaGln Pro Gly Ala Glu 20 25 30 Gly Gly Gly Asp Arg Gly Leu Gly Asp Arg ProAla Pro Lys Asp 35 40 45 Lys Trp Ser Asn Phe Asp Pro Thr Gly Leu Glu ArgAla Ala Lys 50 55 60 Ala Ala Arg Glu Leu Glu His Ser Arg Tyr Ala Lys AspAla Leu 65 70 75 Asn Leu Ala Gln Met Gln Glu Gln Thr Leu Gln Leu Glu GlnGln 80 85 90 Ser Lys Leu Lys Glu Tyr Glu Ala Ala Val Glu Gln Leu Lys Ser95 100 105 Glu Gln Ile Arg Ala Gln Ala Glu Glu Arg Arg Lys Thr Leu Ser110 115 120 Glu Glu Thr Arg Gln His Gln Ala Arg Ala Gln Tyr Gln Asp Lys125 130 135 Leu Ala Arg Gln Arg Tyr Glu Asp Gln Leu Lys Gln Gln Gln Leu140 145 150 Leu Asn Glu Glu Asn Leu Arg Lys Gln Glu Glu Ser Val Gln Lys155 160 165 Gln Glu Ala Met Arg Arg Ala Thr Val Glu Arg Glu Met Glu Leu170 175 180 Arg His Lys Asn Glu Met Leu Arg Val Glu Ala Glu Ala Arg Ala185 190 195 Arg Ala Lys Ala Glu Arg Glu Asn Ala Asp Ile Ile Arg Glu Gln200 205 210 Ile Arg Leu Lys Ala Ala Glu His Arg Gln Thr Val Leu Glu Ser215 220 225 Ile Arg Thr Ala Gly Thr Leu Phe Gly Glu Gly Phe Arg Ala Phe230 235 240 Val Thr Asp Trp Asp Lys Val Thr Ala Thr Val Ala Gly Leu Thr245 250 255 Leu Leu Ala Val Gly Val Tyr Ser Ala Lys Asn Ala Thr Leu Val260 265 270 Ala Gly Arg Phe Ile Glu Ala Arg Leu Gly Lys Pro Ser Leu Val275 280 285 Arg Glu Thr Ser Arg Ile Thr Val Leu Glu Ala Leu Arg His Pro290 295 300 Ile Gln Val Ser Arg Arg Leu Leu Ser Arg Pro Gln Asp Ala Leu305 310 315 Glu Gly Val Val Leu Ser Pro Ser Leu Glu Ala Arg Val Arg Asp320 325 330 Ile Ala Ile Ala Thr Arg Asn Thr Lys Lys Asn Arg Ser Leu Tyr335 340 345 Arg Asn Ile Leu Met Tyr Gly Pro Pro Gly Thr Gly Lys Thr Leu350 355 360 Phe Ala Lys Lys Leu Ala Leu His Ser Gly Met Asp Tyr Ala Ile365 370 375 Met Thr Gly Gly Asp Val Ala Pro Met Gly Arg Glu Gly Val Thr380 385 390 Ala Met His Lys Leu Phe Asp Trp Ala Asn Thr Ser Arg Arg Gly395 400 405 Leu Leu Leu Phe Met Asp Glu Ala Asp Ala Phe Leu Arg Lys Arg410 415 420 Ala Thr Glu Glu Ile Ser Lys Asp Leu Arg Ala Thr Leu Asn Ala425 430 435 Phe Leu Tyr His Met Gly Gln His Ser Asn Lys Phe Met Leu Val440 445 450 Leu Ala Ser Asn Leu Pro Glu Gln Phe Asp Cys Ala Ile Asn Ser455 460 465 Arg Ile Asp Val Met Val His Phe Asp Leu Pro Gln Gln Glu Glu470 475 480 Arg Glu Arg Leu Val Arg Leu His Phe Asp Asn Cys Val Leu Lys485 490 495 Pro Ala Thr Glu Gly Lys Arg Arg Leu Lys Leu Ala Gln Phe Asp500 505 510 Tyr Gly Arg Lys Cys Ser Glu Val Ala Arg Leu Thr Glu Gly Met515 520 525 Ser Gly Arg Glu Ile Ala Gln Leu Ala Val Ser Trp Gln Ala Thr530 535 540 Ala Tyr Ala Ser Lys Asp Gly Val Leu Thr Glu Ala Met Met Asp545 550 555 Ala Cys Val Gln Asp Ala Val Gln Gln Tyr Arg Gln Lys Met Arg560 565 570 Trp Leu Lys Ala Glu Gly Pro Gly Arg Gly Val Glu His Pro Leu575 580 585 Ser Gly Val Gln Gly Glu Thr Leu Thr Ser Trp Ser Leu Ala Thr590 595 600 Gly Pro Ser Tyr Pro Cys Leu Ala Gly Pro Cys Thr Phe Arg Ile605 610 615 Cys Ser Trp Met Gly Thr Gly Leu Cys Pro Gly Pro Leu Ser Pro620 625 630 Arg Met Ser Cys Gly Gly Gly Arg Pro Phe Cys Pro Pro Gly His635 640 645 Pro Leu Leu <210> SEQ ID NO 5 <211> LENGTH: 164 <212> TYPE:PRT <213> ORGANISM: Homo sapiens <220> FEATURE: <221> NAME/KEY:misc_feature <223> OTHER INFORMATION: Incyte ID No: 7503563CD1 <400>SEQUENCE: 5 Met Lys Leu Tyr Ser Leu Ser Val Leu Tyr Lys Gly Glu Ala Lys1 5 10 15 Val Val Leu Leu Lys Ala Ala Tyr Asp Val Ser Ser Phe Ser Phe 2025 30 Phe Gln Arg Ser Ser Val Gln Glu Phe Met Thr Phe Thr Ser Gln 35 4045 Leu Ile Val Glu Arg Ser Ser Lys Gly Thr Arg Ala Ser Val Lys 50 55 60Glu Gln Asp Tyr Leu Cys His Val Tyr Val Arg Asn Asp Ser Leu 65 70 75 AlaGly Val Val Ile Ala Asp Asn Glu Tyr Pro Ser Arg Val Ala 80 85 90 Phe ThrLeu Leu Glu Lys Val Leu Asp Glu Phe Ser Lys Gln Val 95 100 105 Asp ArgIle Asp Trp Pro Val Gly Ser Pro Ala Thr Ile His Tyr 110 115 120 Pro AlaLeu Asp Gly His Leu Ser Arg Tyr Gln Asn Pro Arg Glu 125 130 135 Ala AspPro Met Thr Lys Val Gln Ala Glu Leu Asp Glu Thr Lys 140 145 150 Ile IleLeu Ala Arg Lys Gln Asn Ser Cys Cys Ala Ile Met 155 160 <210> SEQ ID NO6 <211> LENGTH: 702 <212> TYPE: PRT <213> ORGANISM: Homo sapiens <220>FEATURE: <221> NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte IDNo: 6244251CD1 <400> SEQUENCE: 6 Met Trp Pro Gln Pro Cys Leu Pro Pro HisPro Thr Met Leu Glu 1 5 10 15 Glu Thr Gln Gln Ser Lys Leu Ala Ala AlaLys Lys Lys Leu Lys 20 25 30 Glu Tyr Gln Gln Arg Asn Ser Pro Gly Val ProAla Gly Val Lys 35 40 45 Met Lys Lys Lys Asn Thr Gly Ser Ser Pro Glu ThrAla Thr Phe 50 55 60 Gly Gly Cys His Ser Pro Gly Gln Ser Arg Tyr Gln GluLeu Glu 65 70 75 Leu Ala Leu Asp Ser Ser Ser Ala Ile Ile Asn Gln Leu AsnGlu 80 85 90 Asn Ile Glu Ser Leu Lys Gln Gln Lys Lys Gln Val Glu His Gln95 100 105 Leu Glu Glu Val Lys Lys Thr Asn Ser Glu Ile His Lys Ala Gln110 115 120 Met Glu Gln Leu Glu Ala Ile Asp Ile Leu Thr Leu Glu Lys Ala125 130 135 Asp Leu Lys Thr Thr Leu Tyr His Thr Lys Arg Ala Ala Arg His140 145 150 Phe Glu Glu Glu Ser Lys Asp Leu Ala Gly Arg Leu Gln Tyr Ser155 160 165 Leu Gln Arg Ile Gln Glu Leu Glu Arg Ala Leu Cys Ala Val Ser170 175 180 Thr Gln Gln Gln Glu Glu Asp Arg Ser Ser Ser Cys Arg Glu Ala185 190 195 Val Leu His Arg Arg Leu Gln Gln Thr Ile Lys Glu Arg Ala Leu200 205 210 Leu Asn Ala His Val Thr Gln Val Thr Glu Ser Leu Lys Gln Val215 220 225 Gln Leu Glu Arg Asp Glu Tyr Ala Lys His Ile Lys Gly Glu Arg230 235 240 Ala Arg Trp Gln Glu Arg Met Trp Lys Met Ser Val Glu Ala Arg245 250 255 Thr Leu Lys Glu Glu Lys Lys Arg Asp Ile His Arg Ile Gln Glu260 265 270 Leu Glu Arg Ser Leu Ser Glu Leu Lys Asn Gln Met Ala Glu Pro275 280 285 Pro Ser Leu Ala Pro Pro Ala Val Thr Ser Val Val Glu Gln Leu290 295 300 Gln Asp Glu Ala Lys His Leu Arg Gln Glu Val Glu Gly Leu Glu305 310 315 Gly Lys Leu Gln Ser Gln Val Glu Asn Asn Gln Ala Leu Ser Leu320 325 330 Leu Ser Lys Glu Gln Lys Gln Arg Leu Gln Glu Gln Glu Glu Met335 340 345 Leu Arg Glu Gln Glu Ala Gln Arg Val Arg Glu Gln Glu Arg Leu350 355 360 Cys Glu Gln Asn Glu Arg Leu Arg Glu Gln Gln Lys Thr Leu Gln365 370 375 Glu Gln Gly Glu Arg Leu Arg Lys Gln Glu Gln Arg Leu Arg Lys380 385 390 Gln Glu Glu Arg Leu Arg Lys Glu Glu Glu Arg Leu Arg Lys Gln395 400 405 Glu Lys Arg Leu Trp Asp Gln Glu Glu Arg Leu Trp Asp Gln Glu410 415 420 Glu Arg Leu Trp Glu Lys Glu Glu Arg Leu Gln Lys Gln Glu Glu425 430 435 Arg Leu Ala Leu Ser Gln Asn His Lys Leu Asp Lys Gln Leu Ala440 445 450 Glu Pro Gln Cys Ser Phe Glu Asp Leu Asn Asn Glu Asn Lys Ser455 460 465 Ala Leu Gln Leu Glu Gln Gln Val Lys Glu Leu Gln Glu Arg Leu470 475 480 Gly Glu Lys Glu Thr Val Thr Ser Ala Pro Ser Lys Lys Gly Trp485 490 495 Glu Val Gly Thr Ser Leu Trp Gly Gly Glu Leu Pro Thr Gly Asp500 505 510 Gly Gly Gln His Leu Asp Ser Glu Glu Glu Glu Ala Pro Arg Pro515 520 525 Thr Pro Asn Ile Pro Glu Asp Leu Glu Ser Arg Glu Ala Thr Ser530 535 540 Ser Phe Met Asp Leu Pro Lys Glu Lys Ala Asp Gly Thr Glu Gln545 550 555 Val Glu Arg Arg Glu Leu Gly Phe Val Gln Pro Ser Val Ile Val560 565 570 Thr Asp Gly Met Arg Glu Ser Phe Thr Val Tyr Glu Ser Gln Gly575 580 585 Ala Val Pro Asn Thr Arg His Gln Glu Met Glu Asp Phe Ile Arg590 595 600 Leu Ala Gln Lys Glu Glu Glu Met Lys Val Lys Leu Leu Glu Leu605 610 615 Gln Glu Leu Val Leu Pro Leu Val Gly Asp His Glu Gly His Gly620 625 630 Lys Phe Leu Ile Ala Ala Gln Asn Pro Ala Asp Glu Pro Thr Pro635 640 645 Gly Ala Pro Ala Pro Gln Glu Leu Gly Ala Ala Gly Glu Gln Asp650 655 660 Val Phe Tyr Glu Val Ser Leu Asp Asn Asn Val Glu Pro Ala Pro665 670 675 Gly Ala Ala Arg Glu Gly Ser Pro His Asp Asn Pro Thr Val Gln680 685 690 Gln Ile Val Gln Leu Ser Pro Val Met Gln Asp Thr 695 700<210> SEQ ID NO 7 <211> LENGTH: 137 <212> TYPE: PRT <213> ORGANISM: Homosapiens <220> FEATURE: <221> NAME/KEY: misc_feature <223> OTHERINFORMATION: Incyte ID No: 7503467CD1 <400> SEQUENCE: 7 Met Pro Ala ProIle Arg Leu Arg Glu Leu Ile Arg Thr Ile Arg 1 5 10 15 Thr Ala Arg ThrGln Ala Glu Glu Arg Glu Met Ile Gln Lys Glu 20 25 30 Cys Ala Ala Ile ArgSer Ser Phe Arg Glu Glu Asp Asn Thr Tyr 35 40 45 Arg Cys Arg Asn Val AlaLys Leu Leu Tyr Met His Met Leu Gly 50 55 60 Tyr Pro Ala His Phe Gly GlnLeu Glu Cys Leu Lys Leu Ile Ala 65 70 75 Ser Gln Lys Phe Thr Asp Lys ArgIle Val Pro Ala Phe Asn Thr 80 85 90 Gly Thr Ile Thr Gln Val Ile Lys ValLeu Asn Pro Gln Lys Gln 95 100 105 Gln Leu Arg Met Arg Ile Lys Leu ThrTyr Asn His Lys Gly Ser 110 115 120 Ala Met Gln Asp Leu Ala Glu Val AsnAsn Phe Pro Pro Gln Ser 125 130 135 Trp Gln <210> SEQ ID NO 8 <211>LENGTH: 256 <212> TYPE: PRT <213> ORGANISM: Homo sapiens <220> FEATURE:<221> NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte ID No:6599034CD1 <400> SEQUENCE: 8 Met Ala Pro Pro Ala Pro Gly Pro Ala Ser GlyGly Ser Gly Glu 1 5 10 15 Val Asp Glu Leu Phe Asp Val Lys Asn Ala PheTyr Ile Gly Ser 20 25 30 Tyr Gln Gln Cys Ile Asn Glu Ala Gln Arg Val LysLeu Ser Ser 35 40 45 Pro Glu Arg Asp Val Glu Arg Asp Val Phe Leu Tyr ArgAla Tyr 50 55 60 Leu Ala Gln Arg Lys Phe Gly Val Val Leu Asp Glu Ile LysPro 65 70 75 Ser Ser Ala Pro Glu Leu Gln Ala Val Arg Met Phe Ala Asp Tyr80 85 90 Leu Ala His Glu Ser Arg Arg Asp Ser Ile Val Ala Glu Leu Asp 95100 105 Arg Glu Met Ser Arg Ser Val Asp Val Thr Asn Thr Thr Phe Leu 110115 120 Leu Met Ala Ala Ser Ile Tyr Leu His Asp Gln Asn Pro Asp Ala 125130 135 Ala Leu Arg Ala Leu His Gln Gly Asp Ser Leu Glu Cys Thr Ala 140145 150 Met Thr Val Gln Ile Leu Leu Lys Leu Asp Arg Leu Asp Leu Ala 155160 165 Arg Lys Glu Leu Lys Arg Met Gln Asp Leu Asp Glu Asp Ala Thr 170175 180 Leu Thr Gln Leu Ala Thr Ala Trp Val Ser Leu Ala Thr Asp Ser 185190 195 Gly Tyr Pro Glu Thr Leu Val Asn Leu Ile Val Leu Ser Gln His 200205 210 Leu Gly Lys Pro Pro Glu Val Thr Asn Arg Tyr Leu Ser Gln Leu 215220 225 Lys Asp Ala His Arg Ser His Pro Phe Ile Lys Glu Tyr Gln Ala 230235 240 Lys Glu Asn Asp Phe Asp Arg Leu Val Leu Gln Tyr Ala Pro Ser 245250 255 Ala <210> SEQ ID NO 9 <211> LENGTH: 92 <212> TYPE: PRT <213>ORGANISM: Homo sapiens <220> FEATURE: <221> NAME/KEY: misc_feature <223>OTHER INFORMATION: Incyte ID No: 7504179CD1 <400> SEQUENCE: 9 Met PheArg Asn Phe Lys Ile Ile Tyr Arg Arg Tyr Ala Gly Leu 1 5 10 15 Tyr PheCys Ile Cys Val Asp Val Asn Asp Asn Asn Leu Ala Tyr 20 25 30 Leu Glu AlaIle His Asn Phe Val Glu Val Leu Asn Glu Tyr Phe 35 40 45 His Asn Val CysGlu Leu Asp Leu Val Phe Asn Phe Tyr Lys Val 50 55 60 Tyr Thr Val Val AspGlu Met Phe Leu Ala Gly Glu Ile Arg Glu 65 70 75 Thr Ser Gln Thr Lys ValLeu Lys Gln Leu Leu Met Leu Gln Ser 80 85 90 Leu Glu <210> SEQ ID NO 10<211> LENGTH: 610 <212> TYPE: PRT <213> ORGANISM: Homo sapiens <220>FEATURE: <221> NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte IDNo: 71249354CD1 <400> SEQUENCE: 10 Met Ser Gly Gln Ser Leu Thr Asp ArgIle Thr Ala Ala Gln His 1 5 10 15 Ser Val Thr Gly Ser Ala Val Ser LysThr Val Cys Lys Ala Thr 20 25 30 Thr His Glu Ile Met Gly Pro Lys Lys LysHis Leu Asp Tyr Leu 35 40 45 Ile Gln Cys Thr Asn Glu Met Asn Val Asn IlePro Gln Leu Ala 50 55 60 Asp Ser Leu Phe Glu Arg Thr Thr Asn Ser Ser TrpVal Val Val 65 70 75 Phe Lys Ser Leu Ile Thr Thr His His Leu Met Val TyrGly Asn 80 85 90 Glu Arg Phe Ile Gln Tyr Leu Ala Ser Arg Asn Thr Leu PheAsn 95 100 105 Leu Ser Asn Phe Leu Asp Lys Ser Gly Leu Gln Gly Tyr AspMet 110 115 120 Ser Thr Phe Ile Arg Arg Tyr Ser Arg Tyr Leu Asn Glu LysAla 125 130 135 Val Ser Tyr Arg Gln Val Ala Phe Asp Phe Thr Lys Val LysArg 140 145 150 Gly Ala Asp Gly Val Met Arg Thr Met Asn Thr Glu Lys LeuLeu 155 160 165 Lys Thr Val Pro Ile Ile Gln Asn Gln Met Asp Ala Leu LeuAsp 170 175 180 Phe Asn Val Asn Ser Asn Glu Leu Thr Asn Gly Val Ile AsnAla 185 190 195 Ala Phe Met Leu Leu Phe Lys Asp Ala Ile Arg Leu Phe AlaAla 200 205 210 Tyr Asn Glu Gly Ile Ile Asn Leu Leu Glu Lys Tyr Phe AspMet 215 220 225 Lys Lys Asn Gln Cys Lys Glu Gly Leu Asp Ile Tyr Lys LysPhe 230 235 240 Leu Thr Arg Met Thr Arg Ile Ser Glu Phe Leu Lys Val AlaGlu 245 250 255 Gln Val Gly Ile Asp Arg Gly Asp Ile Pro Asp Leu Ser GlnAla 260 265 270 Pro Ser Ser Leu Leu Asp Ala Leu Glu Gln His Leu Ala SerLeu 275 280 285 Glu Gly Lys Lys Ile Lys Asp Ser Thr Ala Ala Ser Arg AlaThr 290 295 300 Thr Leu Ser Asn Ala Val Ser Ser Leu Ala Ser Thr Gly LeuSer 305 310 315 Leu Thr Lys Val Asp Glu Arg Glu Lys Gln Ala Ala Leu GluGlu 320 325 330 Glu Gln Ala Arg Leu Lys Ala Leu Lys Glu Gln Arg Leu LysGlu 335 340 345 Leu Ala Lys Lys Pro His Thr Ser Leu Thr Thr Ala Ala SerPro 350 355 360 Val Ser Thr Ser Ala Gly Gly Ile Met Thr Ala Pro Ala IleAsp 365 370 375 Ile Phe Ser Thr Pro Ser Ser Ser Asn Ser Thr Ser Lys LeuPro 380 385 390 Asn Asp Leu Leu Asp Leu Gln Gln Pro Thr Phe His Pro SerVal 395 400 405 His Pro Met Ser Thr Ala Ser Gln Val Ala Ser Thr Trp GlyGly 410 415 420 Phe Thr Pro Ser Pro Val Ala Gln Pro His Pro Ser Ala GlyLeu 425 430 435 Asn Val Asp Phe Glu Ser Val Phe Gly Asn Lys Ser Thr AsnVal 440 445 450 Ile Val Asp Ser Gly Gly Phe Asp Glu Leu Gly Gly Leu LeuLys 455 460 465 Pro Thr Val Ala Ser Gln Asn Gln Asn Leu Pro Val Ala LysLeu 470 475 480 Pro Pro Ser Lys Leu Val Ser Asp Asp Leu Asp Ser Ser LeuAla 485 490 495 Asn Leu Val Gly Asn Leu Gly Ile Gly Asn Gly Thr Thr LysAsn 500 505 510 Asp Val Asn Trp Ser Gln Pro Gly Glu Lys Lys Leu Thr GlyGly 515 520 525 Ser Asn Trp Gln Pro Lys Val Ala Pro Thr Thr Ala Trp AsnAla 530 535 540 Ala Thr Met Asn Gly Met His Phe Pro Gln Tyr Ala Pro ProVal 545 550 555 Met Ala Tyr Pro Ala Thr Thr Pro Thr Gly Met Ile Gly TyrGly 560 565 570 Ile Pro Pro Gln Met Gly Ser Val Pro Val Met Thr Gln ProThr 575 580 585 Leu Ile Tyr Ser Gln Pro Val Met Arg Pro Pro Asn Pro PheGly 590 595 600 Pro Val Ser Gly Ala Gln Ile Gln Phe Met 605 610 <210>SEQ ID NO 11 <211> LENGTH: 53 <212> TYPE: PRT <213> ORGANISM: Homosapiens <220> FEATURE: <221> NAME/KEY: misc_feature <223> OTHERINFORMATION: Incyte ID No: 7505803CD1 <400> SEQUENCE: 11 Met Ser Arg GlnAla Asn Arg Gly Thr Glu Ser Lys Lys Met Val 1 5 10 15 Gln Met Ala ValGlu Ala Lys Phe Val Gln Asp Thr Leu Lys Gly 20 25 30 Asp Gly Val Thr GluIle Arg Met Arg Phe Ile Arg Arg Ile Glu 35 40 45 Asp Asn Leu Pro Ala GlyGlu Glu 50 <210> SEQ ID NO 12 <211> LENGTH: 137 <212> TYPE: PRT <213>ORGANISM: Homo sapiens <220> FEATURE: <221> NAME/KEY: misc_feature <223>OTHER INFORMATION: Incyte ID No: 7505804CD1 <400> SEQUENCE: 12 Met AlaAsp Phe Asp Glu Ile Tyr Glu Glu Glu Glu Asp Glu Glu 1 5 10 15 Arg AlaLeu Glu Glu Gln Leu Leu Lys Tyr Ser Pro Asp Pro Val 20 25 30 Val Val ArgGly Ser Gly His Val Thr Val Phe Gly Leu Ser Asn 35 40 45 Lys Phe Glu SerGlu Phe Pro Ser Ser Leu Thr Gly Lys Val Ala 50 55 60 Pro Glu Glu Phe LysAla Ser Ile Asn Arg Val Asn Ser Cys Leu 65 70 75 Lys Lys Asn Leu Pro ValAsn Thr Arg Arg Ser Ile Glu Lys Leu 80 85 90 Leu Glu Trp Glu Asn Asn ArgLeu Tyr His Lys Leu Cys Leu His 95 100 105 Trp Arg Leu Ser Lys Arg LysCys Glu Thr Asn Asn Met Met Glu 110 115 120 Tyr Val Ile Leu Ile Glu PheLeu Pro Lys Thr Pro Ile Phe Arg 125 130 135 Pro Asp <210> SEQ ID NO 13<211> LENGTH: 130 <212> TYPE: PRT <213> ORGANISM: Homo sapiens <220>FEATURE: <221> NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte IDNo: 7505846CD1 <400> SEQUENCE: 13 Met Ser Gly Gln Ser Leu Thr Asp ArgIle Thr Ala Ala Gln His 1 5 10 15 Ser Val Thr Gly Ser Ala Val Ser LysThr Val Cys Lys Ala Thr 20 25 30 Thr His Glu Ile Met Gly Pro Lys Lys LysHis Leu Asp Tyr Leu 35 40 45 Ile Gln Cys Thr Asn Glu Met Asn Val Asn IlePro Gln Leu Ala 50 55 60 Asp Ser Leu Phe Glu Arg Thr Thr Asn Ser Ser TrpVal Val Val 65 70 75 Phe Lys Ser Leu Ile Thr Thr His His Leu Met Val TyrGly Asn 80 85 90 Glu Pro Pro Gln Met Gly Ser Val Pro Val Met Thr Gln ProThr 95 100 105 Leu Ile Tyr Ser Gln Pro Val Met Arg Pro Pro Asn Pro PheGly 110 115 120 Pro Val Ser Gly Ala Gln Ile Gln Phe Met 125 130 <210>SEQ ID NO 14 <211> LENGTH: 2852 <212> TYPE: PRT <213> ORGANISM: Homosapiens <220> FEATURE: <221> NAME/KEY: misc_feature <223> OTHERINFORMATION: Incyte ID No: 55004585CD1 <400> SEQUENCE: 14 Met Ala SerGlu Asp Asn Arg Val Pro Ser Pro Pro Pro Thr Gly 1 5 10 15 Asp Asp GlyGly Gly Gly Gly Arg Glu Glu Thr Pro Thr Glu Gly 20 25 30 Gly Ala Leu SerLeu Lys Pro Gly Leu Pro Ile Arg Gly Ile Arg 35 40 45 Met Lys Phe Ala ValLeu Thr Gly Leu Val Glu Val Gly Glu Val 50 55 60 Ser Asn Arg Asp Ile ValGlu Thr Val Phe Asn Leu Leu Val Gly 65 70 75 Gly Gln Phe Asp Leu Glu MetAsn Phe Ile Ile Gln Glu Gly Glu 80 85 90 Ser Ile Asn Cys Met Val Asp LeuLeu Glu Lys Cys Asp Ile Thr 95 100 105 Cys Gln Ala Glu Val Trp Ser MetPhe Thr Ala Ile Leu Lys Lys 110 115 120 Ser Ile Arg Asn Leu Gln Val CysThr Glu Val Gly Leu Val Glu 125 130 135 Lys Val Leu Gly Lys Ile Glu LysVal Asp Asn Met Ile Ala Asp 140 145 150 Leu Leu Val Asp Met Leu Gly ValLeu Ala Ser Tyr Asn Leu Thr 155 160 165 Val Arg Glu Leu Lys Leu Phe PheSer Lys Leu Gln Gly Asp Lys 170 175 180 Gly Arg Trp Pro Pro His Ala GlyLys Leu Leu Ser Val Leu Lys 185 190 195 His Met Pro Gln Lys Tyr Gly ProAsp Ala Phe Phe Asn Phe Pro 200 205 210 Gly Lys Ser Ala Ala Ala Ile AlaLeu Pro Pro Ile Ala Lys Trp 215 220 225 Pro Tyr Gln Asn Gly Phe Thr PheHis Thr Trp Leu Arg Met Asp 230 235 240 Pro Val Asn Asn Ile Asn Val AspLys Asp Lys Pro Tyr Leu Tyr 245 250 255 Cys Phe Arg Thr Ser Lys Gly LeuGly Tyr Ser Ala His Phe Val 260 265 270 Gly Gly Cys Leu Ile Val Thr SerIle Lys Ser Lys Gly Lys Gly 275 280 285 Phe Gln His Cys Val Lys Phe AspPhe Lys Pro Gln Lys Trp Tyr 290 295 300 Met Val Thr Ile Val His Ile TyrAsn Arg Trp Lys Asn Ser Glu 305 310 315 Leu Arg Cys Tyr Val Asn Gly GluLeu Ala Ser Tyr Gly Glu Ile 320 325 330 Thr Trp Phe Val Asn Thr Ser AspThr Phe Asp Lys Cys Phe Leu 335 340 345 Gly Ser Ser Glu Thr Ala Asp AlaAsn Arg Val Phe Cys Gly Gln 350 355 360 Met Thr Ala Val Tyr Leu Phe SerGlu Ala Leu Asn Ala Ala Gln 365 370 375 Ile Phe Ala Ile Tyr Gln Leu GlyLeu Gly Tyr Lys Gly Thr Phe 380 385 390 Lys Phe Lys Ala Glu Ser Asp LeuPhe Leu Ala Glu His His Lys 395 400 405 Leu Leu Leu Tyr Asp Gly Lys LeuSer Ser Ala Ile Ala Phe Thr 410 415 420 Tyr Asn Pro Arg Ala Thr Asp AlaGln Leu Cys Leu Glu Ser Ser 425 430 435 Pro Lys Asp Asn Pro Ser Ile PheVal His Ser Pro His Ala Leu 440 445 450 Met Leu Gln Asp Val Lys Ala ValLeu Thr His Ser Ile Gln Ser 455 460 465 Ala Met His Ser Ile Gly Gly ValGln Val Leu Phe Pro Leu Tyr 470 475 480 Ala Gln Leu Asp Tyr Arg Gln TyrLeu Ser Asp Glu Thr Glu Leu 485 490 495 Thr Ile Cys Ser Thr Leu Leu AlaPhe Ile Met Glu Ser Leu Lys 500 505 510 Asn Ser Ile Ala Met Gln Glu GlnMet Leu Ala Cys Lys Gly Phe 515 520 525 Leu Val Ile Gly Tyr Ser Leu GluLys Ser Ser Lys Ser His Val 530 535 540 Ser Arg Ala Val Leu Glu Leu CysLeu Ala Phe Ser Lys Tyr Leu 545 550 555 Ser Asn Leu Gln Asn Gly Met ProLeu Leu Lys Gln Leu Cys Asp 560 565 570 His Val Leu Leu Asn Pro Ala IleTrp Ile His Thr Pro Ala Lys 575 580 585 Val Gln Leu Met Leu Tyr Thr AspLeu Ser Thr Glu Phe Ile Gly 590 595 600 Thr Val Asn Ile Tyr Asn Thr IleArg Arg Val Gly Thr Val Leu 605 610 615 Leu Ile Met His Thr Leu Lys TyrTyr Tyr Trp Ala Val Asn Pro 620 625 630 Gln Asp Arg Ser Gly Ile Thr ProLys Gly Leu Asp Gly Pro Arg 635 640 645 Pro Asn Gln Lys Glu Met Leu SerLeu Arg Ala Phe Leu Leu Met 650 655 660 Phe Ile Lys Gln Leu Val Met LysAsp Ser Gly Val Lys Glu Asp 665 670 675 Glu Leu Gln Ala Ile Leu Asn TyrLeu Leu Thr Met His Glu Asp 680 685 690 Asp Asn Leu Met Asp Val Leu GlnLeu Leu Val Ala Leu Met Ser 695 700 705 Glu His Pro Asn Ser Met Ile ProAla Phe Asp Gln Arg Asn Gly 710 715 720 Leu Arg Val Ile Tyr Lys Leu LeuAla Ser Lys Ser Glu Gly Ile 725 730 735 Arg Val Gln Ala Leu Lys Ala MetGly Tyr Phe Leu Lys His Leu 740 745 750 Ala Pro Lys Arg Lys Ala Glu ValMet Leu Gly His Gly Leu Phe 755 760 765 Ser Leu Leu Ala Glu Arg Leu MetLeu Gln Thr Asn Leu Ile Thr 770 775 780 Met Thr Thr Tyr Asn Val Leu PheGlu Ile Leu Ile Glu Gln Ile 785 790 795 Gly Thr Gln Val Ile His Lys GlnHis Pro Asp Pro Asp Ser Ser 800 805 810 Val Lys Ile Gln Asn Pro Gln IleLeu Lys Val Ile Ala Thr Leu 815 820 825 Leu Arg Asn Ser Pro Gln Cys ProGlu Ser Met Glu Val Arg Arg 830 835 840 Ala Phe Leu Ser Asp Met Ile LysLeu Phe Asn Asn Ser Arg Glu 845 850 855 Asn Arg Arg Ser Leu Leu Gln CysSer Val Trp Gln Glu Trp Met 860 865 870 Leu Ser Leu Cys Tyr Phe Asn ProLys Asn Ser Asp Glu Gln Lys 875 880 885 Ile Thr Glu Met Val Tyr Ala IlePhe Arg Ile Leu Leu Tyr His 890 895 900 Ala Val Lys Tyr Glu Trp Gly GlyTrp Arg Val Trp Val Asp Thr 905 910 915 Leu Ser Ile Thr His Ser Lys ValThr Phe Glu Ile His Lys Glu 920 925 930 Asn Leu Ala Asn Ile Phe Arg GluGln Gln Gly Lys Val Asp Glu 935 940 945 Glu Ile Gly Leu Cys Ser Ser ThrSer Val Gln Ala Ala Ser Gly 950 955 960 Ile Arg Arg Asp Ile Asn Val SerVal Gly Ser Gln Gln Pro Asp 965 970 975 Thr Lys Asp Ser Pro Val Cys ProHis Phe Thr Thr Asn Gly Asn 980 985 990 Glu Asn Ser Ser Ile Glu Lys ThrSer Ser Leu Glu Ser Ala Ser 995 1000 1005 Asn Ile Glu Leu Gln Thr ThrAsn Thr Ser Tyr Glu Glu Met Lys 1010 1015 1020 Ala Glu Gln Glu Asn GlnGlu Leu Pro Asp Glu Gly Thr Leu Glu 1025 1030 1035 Glu Thr Leu Thr AsnGlu Thr Arg Asn Ala Asp Asp Leu Glu Val 1040 1045 1050 Ser Ser Asp IleIle Glu Ala Val Ala Ile Ser Ser Asn Ser Phe 1055 1060 1065 Ile Thr ThrGly Lys Asp Ser Met Thr Val Ser Glu Val Thr Ala 1070 1075 1080 Ser IleSer Ser Pro Ser Glu Glu Asp Gly Ser Glu Met Pro Glu 1085 1090 1095 PheLeu Asp Lys Ser Ile Val Glu Glu Glu Glu Asp Asp Asp Tyr 1100 1105 1110Val Glu Leu Lys Val Glu Gly Ser Pro Thr Glu Glu Ala Asn Leu 1115 11201125 Pro Thr Glu Leu Gln Asp Asn Ser Leu Ser Pro Ala Ala Ser Glu 11301135 1140 Ala Gly Glu Lys Leu Asp Met Phe Gly Asn Asp Asp Lys Leu Ile1145 1150 1155 Phe Gln Glu Gly Lys Pro Val Thr Glu Lys Gln Thr Asp ThrGlu 1160 1165 1170 Thr Gln Asp Ser Lys Asp Ser Gly Ile Gln Thr Met ThrAla Ser 1175 1180 1185 Gly Ser Ser Ala Met Ser Pro Glu Thr Thr Val SerGln Ile Ala 1190 1195 1200 Val Glu Ser Asp Leu Gly Gln Met Leu Glu GluGly Lys Lys Ala 1205 1210 1215 Thr Asn Leu Thr Arg Glu Thr Lys Leu IleAsn Asp Cys His Gly 1220 1225 1230 Ser Val Ser Glu Ala Ser Ser Glu GlnLys Ile Ala Lys Leu Asp 1235 1240 1245 Val Ser Asn Val Ala Thr Asp ThrGlu Arg Leu Glu Leu Lys Ala 1250 1255 1260 Ser Pro Asn Val Glu Ala ProGln Pro His Arg His Val Leu Glu 1265 1270 1275 Ile Ser Arg Gln His GluGln Pro Gly Gln Gly Ile Ala Pro Asp 1280 1285 1290 Ala Val Asn Gly GlnArg Arg Asp Ser Arg Ser Thr Val Phe Arg 1295 1300 1305 Ile Pro Glu PheAsn Trp Ser Gln Met His Gln Arg Leu Leu Thr 1310 1315 1320 Asp Leu LeuPhe Ser Ile Glu Thr Asp Ile Gln Met Trp Arg Ser 1325 1330 1335 His SerThr Lys Thr Val Met Asp Phe Val Asn Ser Ser Asp Asn 1340 1345 1350 ValIle Phe Val His Asn Thr Ile His Leu Ile Ser Gln Val Met 1355 1360 1365Asp Asn Met Val Met Ala Cys Gly Gly Ile Leu Pro Leu Leu Ser 1370 13751380 Ala Ala Thr Ser Ala Thr His Glu Leu Glu Asn Ile Glu Pro Thr 13851390 1395 Gln Gly Leu Ser Ile Glu Ala Ser Val Thr Phe Leu Gln Arg Leu1400 1405 1410 Ile Ser Leu Val Asp Val Leu Ile Phe Ala Ser Ser Leu GlyPhe 1415 1420 1425 Thr Glu Ile Glu Ala Glu Lys Ser Met Ser Ser Gly GlyIle Leu 1430 1435 1440 Arg Gln Cys Leu Arg Leu Val Cys Ala Val Ala ValArg Asn Cys 1445 1450 1455 Leu Glu Cys Gln Gln His Ser Gln Leu Lys ThrArg Gly Asp Lys 1460 1465 1470 Ala Leu Lys Pro Met His Ser Leu Ile ProLeu Gly Lys Ser Ala 1475 1480 1485 Ala Lys Ser Pro Val Asp Ile Val ThrGly Gly Ile Ser Pro Val 1490 1495 1500 Arg Asp Leu Asp Arg Leu Leu GlnAsp Met Asp Ile Asn Arg Leu 1505 1510 1515 Arg Ala Val Val Phe Arg AspIle Glu Asp Ser Lys Gln Ala Gln 1520 1525 1530 Phe Leu Ala Leu Ala ValVal Tyr Phe Ile Ser Val Leu Met Val 1535 1540 1545 Ser Lys Tyr Arg AspIle Leu Glu Pro Gln Asn Glu Arg His Ser 1550 1555 1560 Gln Ser Cys ThrGlu Thr Gly Ser Glu Asn Glu Asn Val Ser Leu 1565 1570 1575 Ser Glu IleThr Pro Ala Ala Phe Ser Thr Leu Thr Thr Ala Ser 1580 1585 1590 Val GluGlu Ser Glu Ser Thr Ser Ser Ala Arg Arg Arg Asp Ser 1595 1600 1605 GlyIle Gly Glu Glu Thr Ala Thr Gly Leu Gly Ser His Val Glu 1610 1615 1620Val Thr Pro His Thr Ala Pro Pro Gly Val Ser Ala Gly Pro Asp 1625 16301635 Ala Ile Ser Glu Val Leu Ser Thr Leu Ser Leu Glu Val Asn Lys 16401645 1650 Ser Pro Glu Thr Lys Asn Asp Arg Gly Asn Asp Leu Asp Thr Lys1655 1660 1665 Ala Thr Pro Ser Val Ser Val Ser Lys Asn Val Asn Val LysAsp 1670 1675 1680 Ile Leu Arg Ser Leu Val Asn Ile Pro Ala Asp Gly ValThr Val 1685 1690 1695 Asp Pro Ala Leu Leu Pro Pro Ala Cys Leu Gly AlaLeu Gly Asp 1700 1705 1710 Leu Ser Val Glu Gln Pro Val Gln Phe Arg SerPhe Asp Arg Ser 1715 1720 1725 Val Ile Val Ala Ala Lys Lys Ser Ala ValSer Pro Ser Thr Phe 1730 1735 1740 Asn Thr Ser Ile Pro Thr Asn Ala ValSer Val Val Ser Ser Val 1745 1750 1755 Asp Ser Ala Gln Ala Ser Asp MetGly Gly Glu Ser Pro Gly Ser 1760 1765 1770 Arg Ser Ser Asn Ala Lys LeuPro Ser Val Pro Thr Val Asp Ser 1775 1780 1785 Val Ser Gln Asp Pro ValSer Asn Met Ser Ile Thr Glu Arg Leu 1790 1795 1800 Glu His Ala Leu GluLys Ala Ala Pro Leu Leu Arg Glu Ile Phe 1805 1810 1815 Val Asp Phe AlaPro Phe Leu Ser Arg Thr Leu Leu Gly Ser His 1820 1825 1830 Gly Gln GluLeu Leu Ile Glu Gly Thr Ser Leu Val Cys Met Lys 1835 1840 1845 Ser SerSer Ser Val Val Glu Leu Val Met Leu Leu Cys Ser Gln 1850 1855 1860 GluTrp Gln Asn Ser Ile Gln Lys Asn Ala Gly Leu Ala Phe Ile 1865 1870 1875Glu Leu Val Asn Glu Gly Arg Leu Leu Ser Gln Thr Met Lys Asp 1880 18851890 His Leu Val Arg Val Ala Asn Glu Ala Glu Phe Ile Leu Ser Arg 18951900 1905 Gln Arg Ala Glu Asp Ile His Arg His Ala Glu Phe Glu Ser Leu1910 1915 1920 Cys Ala Gln Tyr Ser Ala Asp Lys Arg Glu Asp Glu Lys MetCys 1925 1930 1935 Asp His Leu Ile Arg Ala Ala Lys Tyr Arg Asp His ValThr Ala 1940 1945 1950 Thr Gln Leu Ile Gln Lys Ile Ile Asn Ile Leu ThrAsp Lys His 1955 1960 1965 Gly Ala Trp Gly Asn Ser Ala Val Ser Arg ProLeu Glu Phe Trp 1970 1975 1980 Arg Leu Asp Tyr Trp Glu Asp Asp Leu ArgArg Arg Arg Arg Phe 1985 1990 1995 Val Arg Asn Pro Leu Gly Ser Thr HisPro Glu Ala Thr Leu Lys 2000 2005 2010 Thr Ala Val Glu His Ala Thr AspGlu Asp Ile Leu Ala Lys Gly 2015 2020 2025 Lys Gln Ser Ile Arg Ser GlnAla Leu Gly Asn Gln Asn Ser Glu 2030 2035 2040 Asn Glu Ile Leu Leu GluGly Asp Asp Asp Thr Leu Ser Ser Val 2045 2050 2055 Asp Glu Lys Asp LeuGlu Asn Leu Ala Gly Pro Val Ser Leu Ser 2060 2065 2070 Thr Pro Ala GlnLeu Val Ala Pro Ser Val Val Val Lys Gly Thr 2075 2080 2085 Leu Ser ValThr Ser Ser Glu Leu Tyr Phe Glu Val Asp Glu Glu 2090 2095 2100 Asp ProAsn Phe Lys Lys Ile Asp Pro Lys Ile Leu Ala Tyr Thr 2105 2110 2115 GluGly Leu His Gly Lys Trp Leu Phe Thr Glu Ile Arg Ser Ile 2120 2125 2130Phe Ser Arg Arg Tyr Leu Leu Gln Asn Thr Ala Leu Glu Ile Phe 2135 21402145 Met Ala Asn Arg Val Ala Val Met Phe Asn Phe Pro Asp Pro Ala 21502155 2160 Thr Val Lys Lys Val Val Asn Tyr Leu Pro Arg Val Gly Val Gly2165 2170 2175 Thr Ser Phe Gly Leu Pro Gln Thr Arg Arg Ile Ser Leu AlaSer 2180 2185 2190 Pro Arg Gln Leu Phe Lys Ala Ser Asn Met Thr Gln ArgTrp Gln 2195 2200 2205 His Arg Glu Ile Ser Asn Phe Glu Tyr Leu Met PheLeu Asn Thr 2210 2215 2220 Ile Ala Gly Arg Ser Tyr Asn Asp Leu Asn GlnTyr Pro Val Phe 2225 2230 2235 Pro Trp Val Ile Thr Asn Tyr Glu Ser GluGlu Leu Asp Leu Thr 2240 2245 2250 Leu Pro Thr Asn Phe Arg Asp Leu SerLys Pro Ile Gly Ala Leu 2255 2260 2265 Asn Pro Lys Arg Ala Ala Phe PheAla Glu Arg Tyr Glu Ser Trp 2270 2275 2280 Glu Asp Asp Gln Val Pro LysPhe His Tyr Gly Thr His Tyr Ser 2285 2290 2295 Thr Ala Ser Phe Val LeuAla Trp Leu Leu Arg Ile Glu Pro Phe 2300 2305 2310 Thr Thr Tyr Phe LeuAsn Leu Gln Gly Gly Lys Phe Asp His Ala 2315 2320 2325 Asp Arg Thr PheSer Ser Ile Ser Arg Ala Trp Arg Asn Ser Gln 2330 2335 2340 Arg Asp ThrSer Asp Ile Lys Glu Leu Ile Pro Glu Phe Tyr Tyr 2345 2350 2355 Leu ProGlu Met Phe Val Asn Phe Asn Asn Tyr Asn Leu Gly Val 2360 2365 2370 MetAsp Asp Gly Thr Val Val Ser Asp Val Glu Leu Pro Pro Trp 2375 2380 2385Ala Lys Thr Ser Glu Glu Phe Val His Ile Asn Arg Leu Ala Leu 2390 23952400 Glu Ser Glu Phe Val Ser Cys Gln Leu His Gln Trp Ile Asp Leu 24052410 2415 Ile Phe Gly Tyr Lys Gln Gln Gly Pro Glu Ala Val Arg Ala Leu2420 2425 2430 Asn Val Phe Tyr Tyr Leu Thr Tyr Glu Gly Ala Val Asn LeuAsn 2435 2440 2445 Ser Ile Thr Asp Pro Val Leu Arg Glu Ala Val Glu AlaGln Ile 2450 2455 2460 Arg Ser Phe Gly Gln Thr Pro Ser Gln Leu Leu IleGlu Pro His 2465 2470 2475 Pro Pro Arg Gly Ser Ala Met Gln Val Ser ProLeu Met Phe Thr 2480 2485 2490 Asp Lys Ala Gln Gln Asp Val Ile Met ValLeu Lys Phe Pro Ser 2495 2500 2505 Asn Ser Pro Val Thr His Val Ala AlaAsn Thr Gln Pro Gly Leu 2510 2515 2520 Ala Thr Pro Ala Val Ile Thr ValThr Ala Asn Arg Leu Phe Ala 2525 2530 2535 Val Asn Lys Trp His Asn LeuPro Ala His Gln Gly Ala Val Gln 2540 2545 2550 Asp Gln Pro Tyr Gln LeuPro Val Glu Ile Asp Pro Leu Ile Ala 2555 2560 2565 Ser Asn Thr Gly MetHis Arg Arg Gln Ile Thr Asp Leu Leu Asp 2570 2575 2580 Gln Ser Ile GlnVal His Ser Gln Cys Phe Val Ile Thr Ser Asp 2585 2590 2595 Asn Arg TyrIle Leu Val Cys Gly Phe Trp Asp Lys Ser Phe Arg 2600 2605 2610 Val TyrSer Thr Asp Thr Gly Arg Leu Ile Gln Val Val Phe Gly 2615 2620 2625 HisTrp Asp Val Val Thr Cys Leu Ala Arg Ser Glu Ser Tyr Ile 2630 2635 2640Gly Gly Asn Cys Tyr Ile Leu Ser Gly Ser Arg Asp Ala Thr Leu 2645 26502655 Leu Leu Trp Tyr Trp Asn Gly Lys Cys Ser Gly Ile Gly Asp Asn 26602665 2670 Pro Gly Ser Glu Thr Ala Ala Pro Arg Ala Ile Leu Thr Gly His2675 2680 2685 Asp Tyr Glu Val Thr Cys Ala Ala Val Cys Ala Glu Leu GlyLeu 2690 2695 2700 Val Leu Ser Gly Ser Gln Glu Gly Pro Cys Leu Ile HisSer Met 2705 2710 2715 Asn Gly Asp Leu Leu Arg Thr Leu Glu Gly Pro GluAsn Cys Leu 2720 2725 2730 Lys Pro Lys Leu Ile Gln Ala Ser Arg Glu GlyHis Cys Val Ile 2735 2740 2745 Phe Tyr Glu Asn Gly Leu Phe Cys Thr PheSer Val Asn Gly Lys 2750 2755 2760 Leu Gln Ala Thr Met Glu Thr Asp AspAsn Ile Arg Ala Ile Gln 2765 2770 2775 Leu Ser Arg Asp Gly Gln Tyr LeuLeu Thr Gly Gly Asp Arg Gly 2780 2785 2790 Val Val Val Val Arg Gln ValLeu Asp Leu Lys Gln Leu Phe Ala 2795 2800 2805 Tyr Pro Gly Cys Asp AlaGly Ile Arg Ala Met Ala Leu Ser Tyr 2810 2815 2820 Asp Gln Arg Cys IleIle Ser Gly Met Ala Ser Gly Ser Ile Val 2825 2830 2835 Leu Phe Tyr AsnAsp Phe Asn Arg Trp His His Glu Tyr Gln Thr 2840 2845 2850 Arg Tyr <210>SEQ ID NO 15 <211> LENGTH: 385 <212> TYPE: PRT <213> ORGANISM: Homosapiens <220> FEATURE: <221> NAME/KEY: misc_feature <223> OTHERINFORMATION: Incyte ID No: 7506012CD1 <400> SEQUENCE: 15 Met Ile Ser GlnPhe Phe Ile Leu Ser Ser Lys Gly Asp Pro Leu 1 5 10 15 Ile Tyr Lys AspPhe Arg Gly Asp Ser Gly Gly Arg Asp Val Ala 20 25 30 Glu Leu Phe Tyr ArgLys Leu Thr Gly Leu Pro Gly Asp Glu Ser 35 40 45 Pro Val Val Met Asp TyrGly Tyr Val Gln Thr Thr Ser Thr Glu 50 55 60 Met Leu Arg Asn Phe Ile GlnThr Glu Ala Val Val Ser Lys Pro 65 70 75 Phe Ser Leu Phe Asp Leu Ser SerVal Gly Leu Phe Gly Ala Glu 80 85 90 Thr Gln Gln Ser Lys Val Ala Pro SerSer Ala Ala Ser Arg Pro 95 100 105 Val Leu Ser Ser Arg Ser Asp Gln SerGln Lys Asn Glu Val Phe 110 115 120 Leu Asp Val Val Glu Arg Leu Ser ValLeu Ile Ala Ser Asn Gly 125 130 135 Ser Leu Leu Lys Val Asp Val Gln GlyGlu Ile Arg Leu Lys Ser 140 145 150 Phe Leu Pro Ser Gly Ser Glu Met ArgIle Gly Leu Thr Glu Glu 155 160 165 Phe Cys Val Gly Lys Ser Glu Leu ArgGly Tyr Gly Pro Gly Ile 170 175 180 Arg Val Asp Glu Val Ser Phe His SerSer Val Asn Leu Asp Glu 185 190 195 Phe Glu Ser His Arg Ile Leu Arg LeuGln Pro Pro Gln Gly Glu 200 205 210 Leu Thr Val Met Arg Tyr Gln Leu SerAsp Asp Leu Pro Ser Pro 215 220 225 Leu Pro Phe Arg Leu Phe Pro Ser ValGln Trp Asp Arg Gly Ser 230 235 240 Gly Arg Leu Gln Val Tyr Leu Lys LeuArg Cys Asp Leu Leu Ser 245 250 255 Lys Ser Gln Ala Leu Asn Val Arg LeuHis Leu Pro Leu Pro Arg 260 265 270 Gly Val Val Ser Leu Ser Gln Glu LeuSer Ser Pro Glu Gln Lys 275 280 285 Ala Glu Leu Ala Glu Gly Ala Leu ArgTrp Asp Leu Pro Arg Val 290 295 300 Gln Gly Gly Ser Gln Leu Ser Gly LeuPhe Gln Met Asp Val Pro 305 310 315 Gly Pro Pro Gly Pro Pro Ser His GlyLeu Ser Thr Ser Ala Ser 320 325 330 Pro Leu Gly Leu Gly Pro Ala Ser LeuSer Phe Glu Leu Pro Arg 335 340 345 His Thr Cys Ser Gly Leu Gln Val ArgPhe Leu Arg Leu Ala Phe 350 355 360 Arg Pro Cys Gly Asn Ala Asn Pro HisLys Trp Val Arg His Leu 365 370 375 Ser His Ser Asp Ala Tyr Val Ile ArgIle 380 385 <210> SEQ ID NO 16 <211> LENGTH: 1269 <212> TYPE: PRT <213>ORGANISM: Homo sapiens <220> FEATURE: <221> NAME/KEY: misc_feature <223>OTHER INFORMATION: Incyte ID No: 7506212CD1 <400> SEQUENCE: 16 Met AlaLeu Arg Pro Gly Ala Gly Ser Gly Gly Gly Gly Ala Ala 1 5 10 15 Gly AlaGly Ala Gly Ser Ala Gly Gly Gly Gly Phe Met Phe Pro 20 25 30 Val Ala GlyGly Ile Arg Pro Pro Gln Gly Gly Leu Met Pro Met 35 40 45 Gln Gln Gln GlyPhe Pro Met Val Ser Val Met Gln Pro Asn Met 50 55 60 Gln Gly Ile Met GlyMet Asn Tyr Ser Ser Gln Met Ser Gln Gly 65 70 75 Pro Ile Ala Met Gln AlaGly Ile Pro Met Gly Pro Met Pro Ala 80 85 90 Ala Gly Met Pro Tyr Leu GlyGln Ala Pro Phe Leu Gly Met Arg 95 100 105 Pro Pro Gly Pro Gln Tyr ThrPro Asp Met Gln Lys Gln Phe Ala 110 115 120 Glu Glu Gln Gln Lys Arg PheGlu Gln Gln Gln Lys Leu Leu Glu 125 130 135 Glu Glu Lys Lys Arg Arg GlnPhe Glu Glu Gln Lys Gln Lys Leu 140 145 150 Arg Leu Leu Ser Ser Val LysPro Lys Thr Gly Glu Lys Ser Arg 155 160 165 Asp Asp Ala Leu Glu Ala IleLys Gly Asn Leu Asp Gly Phe Ser 170 175 180 Arg Asp Ala Lys Met His ProThr Pro Ala Ser His Pro Lys Lys 185 190 195 Pro Gly Pro Ser Leu Glu GluLys Phe Leu Val Ser Cys Asp Ile 200 205 210 Ser Thr Ser Gly Gln Glu GlnIle Lys Leu Asn Thr Ser Glu Val 215 220 225 Gly His Lys Ala Leu Gly ProGly Ser Ser Lys Lys Tyr Pro Ser 230 235 240 Leu Met Ala Ser Asn Gly ValAla Val Asp Gly Cys Val Ser Gly 245 250 255 Thr Thr Thr Ala Glu Ala GluAsn Thr Ser Asp Gln Asn Leu Ser 260 265 270 Ile Glu Glu Ser Gly Val GlyVal Phe Pro Ser Gln Asp Pro Ala 275 280 285 Gln Pro Arg Met Pro Pro TrpIle Tyr Asn Glu Ser Leu Val Pro 290 295 300 Asp Ala Tyr Lys Lys Ile LeuGlu Thr Thr Met Thr Pro Thr Gly 305 310 315 Ile Asp Thr Ala Lys Leu TyrPro Ile Leu Met Ser Ser Gly Leu 320 325 330 Pro Arg Glu Thr Leu Gly GlnIle Trp Ala Leu Ala Asn Arg Thr 335 340 345 Thr Pro Gly Lys Leu Thr LysGlu Glu Leu Tyr Thr Val Leu Ala 350 355 360 Met Ile Ala Val Thr Gln LysGly Val Pro Ala Met Ser Pro Asp 365 370 375 Ala Leu Asn Gln Phe Pro AlaAla Pro Ile Pro Thr Leu Ser Gly 380 385 390 Phe Ser Met Thr Leu Pro ThrPro Val Ser Gln Pro Thr Val Ile 395 400 405 Pro Ser Gly Pro Ala Gly SerMet Pro Leu Ser Leu Gly Gln Pro 410 415 420 Val Met Gly Ile Asn Leu ValGly Pro Val Gly Gly Ala Ala Ala 425 430 435 Gln Ala Ser Ser Gly Phe IlePro Thr Tyr Pro Ala Asn Gln Val 440 445 450 Val Lys Pro Glu Glu Asp AspPhe Gln Asp Phe Gln Asp Ala Ser 455 460 465 Lys Ser Gly Ser Leu Asp AspSer Phe Ser Asp Phe Gln Glu Leu 470 475 480 Pro Ala Ser Ser Lys Thr SerAsn Ser Gln His Gly Asn Ser Ala 485 490 495 Pro Ser Leu Leu Met Pro LeuPro Gly Thr Lys Ala Leu Pro Ser 500 505 510 Met Asp Lys Tyr Ala Val PheLys Gly Ile Ala Ala Asp Lys Ser 515 520 525 Ser Glu Asn Thr Val Pro ProGly Asp Pro Gly Asp Lys Tyr Ser 530 535 540 Ala Phe Arg Glu Leu Glu GlnThr Ala Glu Asn Lys Pro Leu Gly 545 550 555 Glu Ser Phe Ala Glu Phe ArgSer Ala Gly Thr Asp Asp Gly Phe 560 565 570 Thr Asp Phe Lys Thr Ala AspSer Val Ser Pro Leu Glu Pro Pro 575 580 585 Thr Lys Asp Lys Thr Phe ProPro Ser Phe Pro Ser Gly Thr Ile 590 595 600 Gln Gln Lys Gln Gln Thr GlnVal Lys Asn Pro Leu Asn Leu Ala 605 610 615 Asp Leu Asp Met Phe Ser SerVal Asn Cys Ser Ser Glu Lys Pro 620 625 630 Leu Ser Phe Ser Ala Val PheSer Thr Ser Lys Ser Val Ser Thr 635 640 645 Pro Gln Ser Thr Gly Ser AlaAla Thr Met Thr Ala Leu Ala Ala 650 655 660 Thr Lys Thr Ser Ser Leu AlaAsp Asp Phe Gly Glu Phe Ser Leu 665 670 675 Phe Gly Glu Tyr Ser Gly LeuAla Pro Val Gly Glu Gln Asp Asp 680 685 690 Phe Ala Asp Phe Met Ala PheSer Asn Ser Ser Ile Ser Ser Glu 695 700 705 Gln Lys Pro Asp Asp Lys TyrAsp Ala Leu Lys Glu Glu Ala Ser 710 715 720 Pro Val Pro Leu Thr Ser AsnVal Gly Ser Thr Val Lys Gly Gly 725 730 735 Gln Asn Ser Thr Ala Ala SerThr Lys Tyr Asp Val Phe Arg Gln 740 745 750 Leu Ser Leu Glu Gly Ser GlyLeu Gly Val Glu Asp Leu Lys Asp 755 760 765 Asn Thr Pro Ser Gly Lys SerAsp Asp Asp Phe Ala Asp Phe His 770 775 780 Ser Ser Lys Phe Ser Ser IleAsn Ser Asp Lys Ser Leu Gly Glu 785 790 795 Lys Ala Val Ala Phe Arg HisThr Lys Glu Asp Ser Ala Ser Val 800 805 810 Lys Ser Leu Asp Leu Pro SerIle Gly Gly Ser Ser Val Gly Lys 815 820 825 Glu Asp Ser Glu Asp Ala LeuSer Val Gln Phe Asp Met Lys Leu 830 835 840 Ala Asp Val Gly Gly Asp LeuLys His Val Met Ser Asp Ser Ser 845 850 855 Leu Asp Leu Pro Thr Val SerGly Gln His Pro Pro Ala Ala Ala 860 865 870 Gly Ser Gly Ser Pro Ser AlaThr Ser Ile Leu Gln Lys Lys Glu 875 880 885 Thr Ser Phe Gly Ser Ser GluAsn Ile Thr Met Thr Ser Leu Ser 890 895 900 Lys Val Thr Thr Phe Val SerGlu Asp Ala Leu Pro Glu Thr Thr 905 910 915 Phe Pro Ala Leu Ala Ser PheLys Asp Thr Ile Pro Gln Thr Ser 920 925 930 Glu Gln Lys Glu Tyr Glu AsnArg Asp Tyr Lys Asp Phe Thr Lys 935 940 945 Gln Asp Leu Pro Thr Ala GluArg Ser Gln Glu Ala Thr Cys Pro 950 955 960 Ser Pro Ala Ser Ser Gly AlaSer Gln Glu Thr Pro Asn Glu Cys 965 970 975 Ser Asp Asp Phe Gly Glu PheGln Ser Glu Lys Pro Lys Ile Ser 980 985 990 Lys Phe Asp Phe Leu Val AlaThr Ser Gln Ser Lys Met Lys Ser 995 1000 1005 Ser Glu Glu Met Ile LysSer Glu Leu Ala Thr Phe Asp Leu Ser 1010 1015 1020 Val Gln Gly Ser HisLys Arg Ser Leu Ser Leu Gly Asp Lys Glu 1025 1030 1035 Ile Ser Arg SerSer Pro Ser Pro Ala Leu Glu Gln Pro Phe Arg 1040 1045 1050 Asp Arg SerAsn Thr Leu Asn Glu Lys Pro Ala Leu Pro Val Ile 1055 1060 1065 Arg AspLys Tyr Lys Asp Leu Thr Gly Glu Val Glu Glu Asn Glu 1070 1075 1080 ArgTyr Ala Tyr Glu Trp Gln Arg Cys Leu Gly Ser Ala Leu Asn 1085 1090 1095Val Ile Lys Lys Ala Asn Asp Thr Leu Asn Gly Ile Ser Ser Ser 1100 11051110 Ser Val Cys Thr Glu Val Ile Gln Ser Ala Gln Gly Met Glu Tyr 11151120 1125 Leu Leu Gly Val Val Glu Val Tyr Arg Val Thr Lys Arg Val Glu1130 1135 1140 Leu Gly Ile Lys Ala Thr Ala Val Cys Ser Glu Lys Leu GlnGln 1145 1150 1155 Leu Leu Lys Asp Ile Asp Lys Val Trp Asn Asn Leu IleGly Phe 1160 1165 1170 Met Ser Leu Ala Thr Leu Thr Pro Asp Glu Asn SerLeu Asp Phe 1175 1180 1185 Ser Ser Cys Met Leu Arg Pro Gly Ile Lys AsnAla Gln Glu Leu 1190 1195 1200 Ala Cys Gly Val Cys Leu Leu Asn Val AspSer Arg Ser Arg Lys 1205 1210 1215 Glu Glu Lys Pro Ala Glu Glu His ProLys Lys Ala Phe Asn Ser 1220 1225 1230 Glu Thr Asp Ser Phe Lys Leu AlaTyr Gly Gly His Gln Tyr His 1235 1240 1245 Ala Ser Cys Ala Asn Phe TrpIle Asn Cys Val Glu Pro Lys Pro 1250 1255 1260 Pro Gly Leu Val Leu ProAsp Leu Leu 1265 <210> SEQ ID NO 17 <211> LENGTH: 394 <212> TYPE: PRT<213> ORGANISM: Homo sapiens <220> FEATURE: <221> NAME/KEY: misc_feature<223> OTHER INFORMATION: Incyte ID No: 7481808CD1 <400> SEQUENCE: 17 MetAla Gly Thr Ala Ala Ala Gly Gly Gln Pro Pro Arg Val Ser 1 5 10 15 MetGln Glu His Met Ala Ile Asp Val Ser Pro Gly Pro Ile Arg 20 25 30 Pro IleArg Leu Ile Ser His Tyr Phe Pro His Phe Tyr Pro Phe 35 40 45 Ala Glu ProAla Leu His Pro Pro Asn Leu Arg Pro Ala Ala Ala 50 55 60 Ser Ala Val ArgSer Ala Pro Gln Leu Gln Pro Asp Pro Glu Pro 65 70 75 Glu Gly Asp Ser AspAsp Ser Thr Ala Leu Gly Thr Leu Glu Phe 80 85 90 Thr Leu Leu Phe Glu AlaAsp Asn Ser Ala Leu His Cys Thr Ala 95 100 105 His Arg Ala Lys Gly LeuLys Pro Leu Ala Ser Gly Ser Ala Asp 110 115 120 Ala Tyr Val Lys Ala AsnLeu Leu Pro Gly Ala Ser Lys Ala Ser 125 130 135 Gln Leu Arg Thr His ThrVal Arg Gly Thr Arg Val Pro Val Trp 140 145 150 Glu Glu Thr Leu Thr TyrHis Gly Phe Thr Arg Gln Asp Ala Glu 155 160 165 Cys Lys Thr Leu Arg SerAsp Leu Gly Gly His Gln Ala Val Cys 170 175 180 Val Arg Gly Pro Met ValGln Arg Gln Trp Gln Ala Pro Ser Leu 185 190 195 Gly Glu Leu Arg Val ProLeu Arg Lys Leu Val Pro Asn Arg Ala 200 205 210 Arg Ser Phe Asp Ile CysLeu Glu Lys Arg Arg Leu Ala Lys Arg 215 220 225 Pro Lys Ser Leu Asp ThrAla Cys Gly Met Ser Leu Tyr Glu Glu 230 235 240 Glu Val Glu Thr Glu ValAla Trp Glu Glu Cys Gly His Val Leu 245 250 255 Leu Ser Leu Cys Tyr SerSer Gln Gln Gly Gly Leu Leu Val Gly 260 265 270 Val Leu Arg Cys Ala HisLeu Ala Pro Met Asp Ala Asn Gly Tyr 275 280 285 Ser Asp Pro Phe Val ArgLeu Phe Leu His Pro Asn Ala Gly Lys 290 295 300 Lys Ser Lys Phe Lys ThrSer Val His Arg Lys Thr Leu Asn Pro 305 310 315 Glu Phe Asn Glu Glu PhePhe Tyr Ser Gly Pro Arg Glu Glu Leu 320 325 330 Ala Gln Lys Thr Leu LeuVal Ser Val Trp Asp Tyr Asp Leu Gly 335 340 345 Thr Ala Asp Asp Phe IleGly Gly Val Gln Leu Gly Ser His Ala 350 355 360 Ser Gly Glu Arg Leu ArgHis Trp Leu Glu Cys Leu Gly His Ser 365 370 375 Asp His Arg Leu Glu LeuTrp His Pro Leu Asp Ser Lys Pro Val 380 385 390 Gln Leu Ser Asp <210>SEQ ID NO 18 <211> LENGTH: 804 <212> TYPE: PRT <213> ORGANISM: Homosapiens <220> FEATURE: <221> NAME/KEY: misc_feature <223> OTHERINFORMATION: Incyte ID No: 7488221CD1 <400> SEQUENCE: 18 Met Ala Glu AsnSer Glu Ser Leu Gly Thr Val Pro Glu His Glu 1 5 10 15 Arg Ile Leu GlnGlu Ile Glu Ser Thr Asp Thr Ala Cys Val Gly 20 25 30 Pro Thr Leu Arg SerVal Tyr Asp Asp Gln Pro Asn Ala His Lys 35 40 45 Lys Phe Met Glu Lys LeuAsp Ala Cys Ile Arg Asn His Asp Lys 50 55 60 Glu Ile Glu Lys Met Cys AsnPhe His His Gln Gly Phe Val Asp 65 70 75 Ala Ile Thr Glu Leu Leu Lys ValArg Thr Asp Ala Glu Lys Leu 80 85 90 Lys Val Gln Val Thr Asp Thr Asn ArgArg Phe Gln Asp Ala Gly 95 100 105 Lys Glu Val Ile Val His Thr Glu AspIle Ile Arg Cys Arg Ile 110 115 120 Gln Gln Arg Asn Ile Thr Thr Val ValGlu Lys Leu Gln Leu Cys 125 130 135 Leu Pro Val Leu Glu Met Tyr Ser LysLeu Lys Glu Gln Met Ser 140 145 150 Ala Lys Arg Tyr Tyr Ser Ala Leu LysThr Met Glu Gln Leu Glu 155 160 165 Asn Val Tyr Phe Pro Trp Val Ser GlnTyr Arg Phe Cys Gln Leu 170 175 180 Met Ile Glu Asn Leu Pro Lys Leu ArgGlu Asp Ile Lys Glu Ile 185 190 195 Ser Met Ser Asp Leu Lys Asp Phe LeuGlu Ser Ile Arg Lys His 200 205 210 Ser Asp Lys Ile Gly Glu Thr Ala MetLys Gln Ala Gln His Gln 215 220 225 Lys Thr Phe Ser Val Ser Leu Gln LysGln Asn Lys Met Lys Phe 230 235 240 Gly Lys Asn Met Tyr Ile Asn Arg AspArg Ile Pro Glu Glu Arg 245 250 255 Asn Glu Thr Val Leu Lys His Ser LeuGlu Glu Glu Asp Glu Asn 260 265 270 Glu Glu Glu Ile Leu Thr Val Gln AspLeu Val Asp Phe Ser Pro 275 280 285 Val Tyr Arg Cys Leu His Ile Tyr SerVal Leu Gly Asp Glu Glu 290 295 300 Thr Phe Glu Asn Tyr Tyr Arg Lys GlnArg Lys Lys Gln Ala Arg 305 310 315 Leu Val Leu Gln Pro Gln Ser Asn MetHis Glu Thr Val Asp Gly 320 325 330 Tyr Arg Arg Tyr Phe Thr Gln Ile ValGly Phe Phe Val Val Glu 335 340 345 Asp His Ile Leu His Val Thr Gln GlyLeu Val Thr Arg Ala Tyr 350 355 360 Thr Asp Glu Leu Trp Asn Met Ala LeuSer Lys Ile Ile Ala Val 365 370 375 Leu Arg Ala His Ser Ser Tyr Cys ThrAsp Pro Asp Leu Val Leu 380 385 390 Glu Leu Lys Asn Leu Ile Val Ile PheAla Asp Thr Leu Gln Gly 395 400 405 Tyr Gly Phe Pro Val Asn Arg Leu PheAsp Leu Leu Phe Glu Ile 410 415 420 Arg Asp Gln Tyr Asn Glu Thr Leu LeuLys Lys Trp Ala Gly Val 425 430 435 Phe Arg Asp Ile Phe Glu Glu Asp AsnTyr Ser Pro Ile Pro Val 440 445 450 Val Asn Glu Glu Glu Tyr Lys Ile ValIle Ser Lys Phe Pro Phe 455 460 465 Gln Asp Pro Asp Leu Glu Lys Gln SerPhe Pro Lys Lys Phe Pro 470 475 480 Met Ser Gln Ser Val Pro His Ile TyrIle Gln Val Lys Glu Phe 485 490 495 Ile Tyr Ala Ser Leu Lys Phe Ser GluSer Leu His Arg Ser Ser 500 505 510 Thr Glu Ile Asp Asp Met Leu Arg LysSer Thr Asn Leu Leu Leu 515 520 525 Thr Arg Thr Leu Ser Ser Cys Leu LeuAsn Leu Ile Arg Lys Pro 530 535 540 His Ile Gly Leu Thr Glu Leu Val GlnIle Ile Ile Asn Thr Thr 545 550 555 His Leu Glu Gln Ala Cys Lys Tyr LeuGlu Asp Phe Ile Thr Asn 560 565 570 Ile Thr Asn Ile Ser Gln Glu Thr ValHis Thr Thr Arg Leu Tyr 575 580 585 Gly Leu Ser Thr Phe Lys Asp Ala ArgHis Ala Ala Glu Gly Glu 590 595 600 Ile Tyr Thr Lys Leu Asn Gln Lys IleAsp Glu Phe Val Gln Leu 605 610 615 Ala Asp Tyr Asp Trp Thr Met Ser GluPro Asp Gly Arg Ala Ser 620 625 630 Gly Tyr Leu Met Asp Leu Ile Asn PheLeu Arg Ser Ile Phe Gln 635 640 645 Val Phe Thr His Leu Pro Gly Lys ValAla Gln Thr Ala Cys Met 650 655 660 Ser Ala Cys Gln His Leu Ser Thr SerLeu Met Gln Met Leu Leu 665 670 675 Asp Ser Glu Leu Lys Gln Ile Ser MetGly Ala Val Gln Gln Phe 680 685 690 Asn Leu Asp Val Ile Gln Cys Glu LeuPhe Ala Ser Ser Glu Pro 695 700 705 Val Pro Gly Phe Gln Gly Asp Thr LeuGln Leu Ala Phe Ile Asp 710 715 720 Leu Arg Gln Leu Leu Asp Leu Phe MetVal Trp Asp Trp Ser Thr 725 730 735 Tyr Leu Ala Asp Tyr Gly Gln Pro AlaSer Lys Tyr Leu Arg Val 740 745 750 Asn Pro Asn Thr Ala Leu Thr Leu LeuGlu Lys Met Lys Asp Thr 755 760 765 Ser Lys Lys Asn Asn Ile Phe Ala GlnPhe Arg Lys Asn Asp Arg 770 775 780 Asp Lys Gln Lys Leu Ile Glu Thr ValVal Lys Gln Leu Arg Ser 785 790 795 Leu Val Asn Gly Met Ser Gln His Met800 <210> SEQ ID NO 19 <211> LENGTH: 137 <212> TYPE: PRT <213> ORGANISM:Homo sapiens <220> FEATURE: <221> NAME/KEY: misc_feature <223> OTHERINFORMATION: Incyte ID No: 7505894CD1 <400> SEQUENCE: 19 Met Pro Ala ProIle Arg Leu Arg Glu Leu Ile Arg Thr Ile Arg 1 5 10 15 Thr Ala Arg ThrGln Ala Glu Glu Arg Glu Met Ile Gln Lys Glu 20 25 30 Cys Ala Ala Ile ArgSer Ser Phe Arg Glu Glu Asp Asn Thr Tyr 35 40 45 Arg Cys Arg Asn Val AlaLys Leu Leu Tyr Met His Met Leu Gly 50 55 60 Tyr Pro Ala His Phe Gly GlnLeu Glu Cys Leu Lys Leu Ile Ala 65 70 75 Ser Gln Lys Phe Thr Asp Lys ArgIle Val Pro Ala Phe Asn Thr 80 85 90 Gly Thr Ile Thr Gln Val Ile Lys ValLeu Asn Pro Gln Lys Gln 95 100 105 Gln Leu Arg Met Arg Ile Lys Leu ThrTyr Asn His Lys Gly Ser 110 115 120 Ala Met Gln Asp Leu Ala Glu Val AsnAsn Phe Pro Pro Gln Ser 125 130 135 Trp Gln <210> SEQ ID NO 20 <211>LENGTH: 262 <212> TYPE: PRT <213> ORGANISM: Homo sapiens <220> FEATURE:<221> NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte ID No:7505901CD1 <400> SEQUENCE: 20 Met Arg Asp Arg Thr His Glu Leu Arg GlnGly Asp Asp Ser Ser 1 5 10 15 Asp Glu Glu Asp Lys Glu Arg Val Ala LeuVal Val His Pro Gly 20 25 30 Thr Ala Arg Leu Gly Ser Pro Asp Glu Glu PhePhe His Lys Val 35 40 45 Arg Thr Ile Arg Gln Thr Ile Val Lys Leu Gly AsnLys Val Gln 50 55 60 Glu Leu Glu Lys Gln Leu Lys Ala Ile Glu Pro Gln LysGlu Glu 65 70 75 Ala Asp Glu Asn Tyr Asn Ser Val Asn Thr Arg Met Arg LysThr 80 85 90 Gln His Gly Val Leu Ser Gln Gln Phe Val Glu Leu Ile Asn Lys95 100 105 Cys Asn Ser Met Gln Ser Glu Tyr Arg Glu Lys Asn Val Glu Arg110 115 120 Ile Arg Arg Gln Leu Lys Ile Thr Asn Ala Gly Met Val Ser Asp125 130 135 Glu Glu Leu Glu Gln Met Leu Asp Ser Gly Gln Ser Glu Val Phe140 145 150 Val Ser Asn Ile Leu Lys Asp Thr Gln Val Thr Arg Gln Ala Leu155 160 165 Asn Glu Ile Ser Ala Arg His Ser Glu Ile Gln Gln Leu Glu Arg170 175 180 Ser Ile Arg Glu Leu His Asp Ile Phe Thr Phe Leu Ala Thr Glu185 190 195 Val Glu Met Gln Gly Glu Met Ile Asn Arg Ile Glu Lys Asn Ile200 205 210 Leu Ser Ser Ala Asp Tyr Val Glu Arg Gly Gln Glu His Val Lys215 220 225 Thr Ala Leu Glu Asn Gln Lys Lys Ala Arg Lys Lys Lys Val Leu230 235 240 Ile Ala Ile Cys Val Ser Ile Thr Val Val Leu Leu Ala Val Ile245 250 255 Ile Gly Val Thr Val Val Gly 260 <210> SEQ ID NO 21 <211>LENGTH: 2251 <212> TYPE: DNA <213> ORGANISM: Homo sapiens <220> FEATURE:<221> NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte ID No:7500521CB1 <400> SEQUENCE: 21 cccacgcgtc cggaggtgtt gggtttgggggacgctggca gctgggttct cccggttccc 60 ttgggcaggt gcagggtcgg gttcaaagcctccggaacgc gttttggcct gatttgagga 120 ggggggcggg gagggacctg cggcttgcggccccgccccc ttctccggct cgcagccgac 180 cggtaagccc gcctcctccc tcggccggccctggggccgt gtccgccggg caactccagc 240 cgaggcctgg gcttctgcct gcaggtgtctgcggcgaggc ccctagggta cagcccgatt 300 tggccccatg gtgggtttcg gggccaaccggcgggctggc cgcctgccct ctctcgtgct 360 ggtggtgctg ctggtggtga tcgtcgtcctcgccttcaac tactggagca tctcctcccg 420 ccacgtcctg cttcaggagg aggtggccgagctgcagggc caggtccagc gcaccgaagt 480 ggcccgcggg cggctggaaa agcgcaattcggacctcttg ctgttggtgg acacgcacaa 540 gaaacagatc gaccagaagg aggccgactacggccgcctc agcagccggc tgcaggccag 600 agagggcctc gggaagagat gcgaggatgacaaggttaaa ctacagaaca acatatcgta 660 tcagatggca gacatacatc atttaaaggagcaacttgct gagcttcgtc aggaatttct 720 tcgacaagaa gaccagcttc aggactataggaagaacaat acttaccttg tgaagaggtt 780 agaatatgaa agttttcagt gtggacagcagatgaaggaa ttgagagcac agcatgaaga 840 aaatattaaa aagttagcag accagtttttagaggaacaa aagcaagaga cccaaaagat 900 tcaatcaaat gatggaaagg aattggatataaacaatcaa gtagtaccta aaaatattcc 960 aaaagtagct gagaatgttg cagataagaatgaagaaccc tcaagcaatc atattccaca 1020 tgggaaagaa caaatcaaaa gaggtggtgatgcagggatg cctggaatag aagagaatga 1080 cctagcaaaa gttgatgatc ttccccctgctttaaggaag cctcctattt cagtttctca 1140 acatgaaagt catcaagcaa tctcccatcttccaactgga caacctctct ccccaaatat 1200 gcctccagat tcacacataa accacaatggaaaccccggt acttcaaaac agaatccttc 1260 cagtcctctt cagcgtttaa ttccaggctcaaacttggac agtgaaccca gaattcaaac 1320 agatatacta aagcaggcta ccaaggacagagtcagtgat ttccataaat tgaagcaaaa 1380 tgatgaagaa cgagagcttc aaatggatcctgcagactat ggaaagcaac atttcaatga 1440 tgtcctttaa gtcctaaagg aatgcttcagaaaacctaaa gtgctgtaaa atgaaatcat 1500 tctactttgt cctttctgac ttttgttgtaaagacgaatt gtatcagttg taaagataca 1560 ttgagataga attaaggaaa aactttaatgaaggaatgta cccatgtaca tatgtgaact 1620 ttttcatatt gtattatcaa ggtatagacttttttggtta tgatacagtt aagccaaaaa 1680 cagctaatct ttgcatctaa agcaaactaatgtatatttc acattttatt gagccgactt 1740 atttccacaa atagataaac aggacaaaatagttgtacag gttatatgtg gcatagcata 1800 accacagtaa gaacagaaca gatattcagcagaaaacttt ttatactcta attctttttt 1860 tttttttttt tgagacagag ttttagtcttgtttcccagg ctggagtgca atggcacaat 1920 cttggctcac tgcaacctcc gcctcctgggttcaggcaat tttcctgcct cagcctccca 1980 agtagctggg attacaggca cccaccaccatgcccagcta atttttgtat ttttaataga 2040 gagctaataa ttgtatattt aataaagacgggtttcacca tgttggccag gctggtcttg 2100 aactcctgac ctcaggtgat cctcctgcattggcctccca aagtgctgga attccaggca 2160 tgagccactg cgcccagtct acacactaattcttgttagc ccaacagctg ttctgttcta 2220 tctacccctc atttcacgct caaggagtca t2251 <210> SEQ ID NO 22 <211> LENGTH: 1775 <212> TYPE: DNA <213>ORGANISM: Homo sapiens <220> FEATURE: <221> NAME/KEY: misc_feature <223>OTHER INFORMATION: Incyte ID No: 7502992CB1 <400> SEQUENCE: 22acgcccgtcg caggctccgc tggccgaccg ctacgcgctg ctgcactggc acaatcaggt 60ctaccccaga gaggtcctag ggctggtgga catggccgcc ctggagaaat ggggagctgg 120ggccccttct ctcccctggc accctgcggg gtttggagga tgaatgcgtc acagatgtta 180aggctcagac ccgggctgcc cttctccgtg tgctgcagga ggacgaagag cactggggga 240gcctggagga ccagcccagc agcctggccc aggatgtgtg tgagctgctg gaagagcaca 300cagagcgagc accccgcatc agccaggagt ttggggagcg gatggcccac tgctgcctag 360gcgggctggc agagttcctg cagagcttcc agcagcgtgt ggagcgattc catgagaacc 420cagcagtccg ggagatgcta cctgacacct atatcagcaa gaccatcgcc ctggtcaact 480gcggcccccc actgagagct ctggccgagc gcctggcccg ggtggggccc ccagaaagcg 540agccggcccg ggaagcatct gctagtgctc tggaccatgt gacccggctc tgccaccgtg 600tcgtggccaa cctgctgttc caggagctgc agccacactt caacaagctg atgcgccgga 660agtggctgag cagcccggag gccctggatg gcatcgtggg cacgctgggt gcccaggccc 720tggccctgcg cagaatgcag gacgagcctt accaggcgct ggtagccgag ctacaccggc 780gggcgctggt cgagtacgtg cggcccctgc tccgtgggcg cctgcgctgc agctcggcgc 840ggacccgcag ccgcgtggcc ggcaggctcc gggaggacgc ggcgcaactg cagaggctgt 900tccggcggct ggagtcccag gcctcgtggc tggatgccgt ggtgccccat ttggctgaag 960tcatgcagct ggaagacacg cccagcatcc aggtggaggt gggagtgttg gtgcgcgact 1020acccagacat caggcagaag cacgtggcag ccctcctcga catccgtggc ctgcgcaaca 1080cagccgcccg ccaggagatc ctggccgtgg cccgggacct ggaactctct gaggagggag 1140ccctgtcacc ccctcgggac cgtgccttct ttgcagacat ccctgtgccc cgcccatctt 1200tctgtctcag cctccctctc ttcctgggcc gcctccccct ctcccggctg gccaggccca 1260gtttggcctg tctgcctcgg ccccggcctc cgtctctagc gcgacctcgg gcccagcgct 1320gagggtcacc caaccgccgg ccttagtgac cccatctatg ctgctgacaa gccaacctcc 1380cgtacggcgc ccctcctgac tccctgcctg ggaccacaca cccctgggat agaaagaccc 1440ttagatgtct tttcacccaa ccccaaactc cctgtacaga agggaaacaa acgccaggca 1500cggtggctca tgcctgtaat cccaacactt tgggaggctg aggccggagg attgcttgag 1560cccaggagtt caagaccagc ctgggcaaca tagtgagacc tgccccctat ctctacaaaa 1620aataaaaaat tagctgggca cggtggtgtg tgcctgtagt cccagctact ggcgaggctg 1680aggctggagg atcactggag ttcgaggctg cagtgagcta tgactgtgcc actgcactcc 1740agcctggtca acaaagcaag accctttctc aaaaa 1775 <210> SEQ ID NO 23 <211>LENGTH: 3959 <212> TYPE: DNA <213> ORGANISM: Homo sapiens <220> FEATURE:<221> NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte ID No:71187173CB1 <400> SEQUENCE: 23 ggagcgcaga gctgcagccg ccgagccggacgtgtccgcg aagatggcgg gccggagcat 60 gcaagcggca agatgtccta cagatgaattatctttaacc aattgtgcag ttgtgaatga 120 aaaggatttc cagtctggcc agcatgtgattgtgaggacc tctcccaatc acaggtacac 180 atttacactg aagacacatc catcggtggttccagggagc attgcattca gtttacctca 240 gagaaaatgg gctgggcttt ctattgggcaagaaatagaa gtctccttat atacatttga 300 caaagccaaa cagtgtattg gcacaatgaccatcgagatt gatttcctgc agaaaaaaag 360 cattgactcc aacccttatg acaccgacaagatggcagca gaatttattc agcaattcaa 420 caaccaggcc ttctcagtgg gacaacagcttgtctttagc ttcaatgaaa agctttttgg 480 cttactggtg aaggacattg aagccatggatcctagcatc ctgaagggag agcctgcgac 540 agggaaaagg cagaagattg aagtaggactggttgttgga aacagtcaag ttgcatttga 600 aaaagcagaa aattcgtcac ttaatcttattggcaaagct aaaaccaagg aaaatcgcca 660 atcaattatc aatcctgact ggaactttgaaaaaatggga ataggaggtc tagacaagga 720 attttcagat attttccgac gagcatttgcttcccgagta tttcctccag agattgtgga 780 gcagatgggt tgtaaacatg ttaaaggcatcctgttatat ggacccccag gttgtggtaa 840 gactctcttg gctcgacaga ttggcaagatgttgaatgca agagagccca aagtggtcaa 900 tgggccagaa atccttaaca aatatgtgggagaatcagag gctaacattc gcaaactttt 960 tgctgatgct gaagaggagc aaaggaggcttggtgctaac agtggtttgc acatcatcat 1020 ctttgatgaa attgatgcca tctgcaagcagagagggagc atggctggta gcacgggagt 1080 tcatgacact gttgtcaacc agttgctgtccaaaattgat ggcgtggagc agctaaacaa 1140 catcctagtc attggaatga ccaatagaccagatctgata gatgaggctc ttcttagacc 1200 tggaagactg gaagttaaaa tggagataggcttgccagat gagaaaggcc gactacagat 1260 tcttcacatc cacacagcaa gaatgagagggcatcagtta ctctctgctg atgtagacat 1320 taaagaactg gccgtggaga ccaagaatttcagtggtgct gaattggagg gtctggtgcg 1380 agcagcccag tccactgcta tgaatagacacataaaggcc agtactaaag tggaagtgga 1440 catggagaaa gcagaaagcc tgcaagtgacgagaggagac ttccttgctt ctttggagaa 1500 tgatatcaaa ccagcctttg gcacaaaccaagaagattat gcaagttata ttatgaacgg 1560 tatcatcaaa tggggtgacc cagttactcgagttctagat gatggggagc tgctggtgca 1620 gcagactaag aacagtgacc gcacaccattggtcagcgtg cttctggaag gccctcctca 1680 cagtgggaag actgctttag ctgcaaaaattgcagaggaa tccaacttcc cgttcatcaa 1740 gatctgttct cctgataaaa tgattggcttttctgaaaca gccaaatgtc aggccatgaa 1800 gaagatcttt gatgatgcgt acaaatcccagctcagttgt gtggttgtgg atgacattga 1860 gagattgctt gattacgtcc ctattggccctcgattttca aatcttgtat tacaggctct 1920 tctcgtttta ctgaaaaagg cacctcctcagggccgcaag cttcttatca ttgggaccac 1980 tagccgcaaa gatgtccttc aggagatggaaatgcttaac gctttcagca ccaccatcca 2040 cgtgcccaac attgccacag gagagcagctgttggaagct ttggagcttt tgggcaactt 2100 caaggataag gaacgcacca caattgcacagcaagtcaaa gggaagaagg tctggatagg 2160 aatcaagaag ttactaatgc tgatcgagatgtccctacag atggatcctg aataccgtgt 2220 gagaaaattc ttggccctct taagagaagaaggagctagc ccccttgatt ttgattgaaa 2280 atgaactatt tgaaacacac agtgaccaagggaagtgacc aaggtgaaga tggcctagga 2340 tcttcactgt cttactcaag atactggactaagtggaacg ttctctacct tcaacatgtg 2400 ctcgctctgc atgattagtg caataaaactcccttcctta tgcatactga gatagcttag 2460 tgtctcgtgg aaggtgtcaa tttggtttagaatgctgcgc ttaccttccc atgcaggcta 2520 aagtgattcc ttcttgctca gtccctctgggtgggaacca tccagtactt gtggacacta 2580 cacgtttcaa cctctctact agcaccatcacccttgaaaa ctctcagtca gtgtcatgaa 2640 tgttgcatga caacagttgg ccgattagaaggcagacttt ctacatgcaa atctggctta 2700 gtaaatcgag gtgtgggcca gagatcctctgacagctgtc ctgagctaac actaaaagtc 2760 actgggtatt tggttaaagg tctcccacaagactggtatt ctctttgcct gaagaaacaa 2820 ggcattgaat ctctaaaatg ctgttctcaatcattgtcag agatgttttc aagttgcagt 2880 cagaagatct ttcttaatag aaagtcagatgactaccgtg ttggttgtga cttcccctta 2940 agtataacta atttgctctg tggtaagagatatgctcatt attaccactt agaagatgtt 3000 gttaaaaaca tgtgaaagat aggtatggaaaaagcataca cccccaaaca gaaaggagtt 3060 attaaagtaa tttacaaacc tctcagcactaattagtgtc caactccaag tgggtcaatt 3120 ccttagtata atattaaggc ttactagtatcactgctttt tccttagctt aatgacttac 3180 ttagaattta tcctttattt taaatgatctgtactatcta gtgtctaaaa cactattctc 3240 cagaaaaatc aatcattttc tagccctctccctcagtcct ttattgtcca ttccaataca 3300 ttgaacacat ttcctttacc ctccacacacttcttccaaa aggaagcacc cgttgagtcc 3360 ttttgagggt gatttgtctt acaactgactgacttagcag gaatttaatt aggtcatatt 3420 tggtgatgag acttatggag tgtgcctctctctcccaact gctgcttaaa atgcaaggac 3480 aagcaattag aagccatcct aaggtgcttacctcacacgc cacccatgag gcttgtggcc 3540 acagtggcac ttgggtgtgg ctcctctgttatttgtcctc atgtgagaaa gcagatcatc 3600 tccaaatctt gccatttgta tacttttggtggagacttgg atgtcatatc ttctttgttt 3660 tgggttttct tccctagctt attttgtggcttttaaagaa gtggattgta ttgtgagatc 3720 ctgtgattcc tggtggccag tatcctggattcctctaaga tcttgcctct ttcctcctca 3780 tgaaagcagc acacattgtg ttaacttatgtctcttgtta aatgagctta atgtctttgt 3840 gttttgtcca aaactgtatt gaaaaaatattgtttaatgc aaatgaagga atgcaataaa 3900 gagtaaatat acttgaaaaa aaaaaaaaaaaaaaaaaaaa aaaaaaaatg gttgcggtc 3959 <211> LENGTH: 2460 <212> TYPE: DNA<213> ORGANISM: Homo sapiens <220> FEATURE: <221> NAME/KEY: misc_feature<223> OTHER INFORMATION: Incyte ID No: 7503143CB1 <400> SEQUENCE: 24ggtgtgtgtg gcgcctgcgc agtggcggtg accaccggct cgcggcgcgt ggaggctgct 60cccagccgcg cgcgagtcag actcgggtgg gggtcccggc ggcggtagcg gcggcggcgg 120tgcgagcatg tcgtggctct tcggcattaa caagggcccc aagggtgaag gcgcggggcc 180gccgccgcct ttgccgcccg cgcagcccgg ggccgagggc ggcggggacc gcgggttggg 240agaccggccg gcgcccaagg acaaatggag caacttcgac cccaccggcc tggagcgcgc 300cgccaaggcg gcgcgcgagc tggagcactc gcgttatgcc aaggacgccc tgaatctggc 360acagatgcag gagcagacgc tgcagttgga gcaacagtcc aagctcaaag agtatgaggc 420cgccgtggag cagctcaaga gcgagcagat ccgggcgcag gctgaggaga ggaggaagac 480cctgagcgag gagacccggc agcaccaggc cagggcccag tatcaagaca agctggcccg 540gcagcgctac gaggaccaac tgaagcagca gcaacttctc aatgaggaga atttacggaa 600gcaggaggag tccgtgcaga agcaggaagc catgcggcga gccaccgtgg agcgggagat 660ggagctgcgg cacaagaatg agatgctgcg agtggaggcc gaggcccggg cgcgcgccaa 720ggccgagcgg gagaatgcag acatcatccg cgagcagatc cgcctgaagg cggccgagca 780ccgtcagacc gtcttggagt ccatcaggac ggctggcacc ttgtttgggg aaggattccg 840tgcctttgtg acagactggg acaaagtgac agccacggtg gctgggctga cgctgctggc 900tgttggggtc tactcagcca agaatgccac gcttgtcgcc ggccgcttca tcgaggctcg 960gctggggaag ccgtccctag tgagggagac gtcccgcatc acggtgcttg aggcgctgcg 1020gcaccccatc caggtcagcc ggcggctcct cagtcgaccc caggacgcgc tggagggtgt 1080tgtgctcagt cccagcctgg aagcacgggt gcgcgacatc gccatagcaa caaggaacac 1140caagaagaac cgcagcctgt acaggaacat cctgatgtac gggccaccag gcaccgggaa 1200gacgctgttt gccaagaaac tcgccctgca ctcaggcatg gactacgcca tcatgacagg 1260cggggacgtg gcccccatgg ggcgggaagg cgtgaccgcc atgcacaagc tctttgactg 1320ggccaatacc agccggcgcg gcctcctgct cttcatggat gaagcggacg ccttccttcg 1380gaagcgagcc actgaggaga taagcaagga cctcagagcc acactgaacg ccttcctgta 1440ccacatgggc caacacagca acaaattcat gctggtcctg gccagcaatc tgcctgagca 1500gttcgactgt gccatcaaca gccgcatcga cgtgatggtc cacttcgacc tgccgcagca 1560ggaggagcgg gagcgcctgg tgagactgca ttttgacaac tgtgttctta agccggccac 1620agaaggaaaa cggcgcctga agctggccca gtttgactac gggaggaagt gctcggaggt 1680cgctcggctg acggagggca tgtcgggccg ggagatcgct cagctggccg tgtcctggca 1740ggccacggca tatgcctcca aggacggggt cctcactgag gccatgatgg acgcctgtgt 1800gcaagatgct gtccagcagt accgacagaa gatgcgctgg ctgaaggcgg aggggcctgg 1860gcgcggggtc gagcaccccc tatccggagt ccaaggcgag accctcacct catggagcct 1920ggccacgggc ccctcctacc cctgccttgc cggcccctgc acatttagga tatgctcctg 1980gatggggact gggctgtgcc cagggcctct gtcccccagg atgtcttgtg gtggcggtcg 2040gccgttctgc cccccagggc accccctgtt gtaggcactg gctagggagg ggcaggcctc 2100cttcctgccc ctcgagacac tcttgggaga tgcattttcc gtctggctca cagggggagg 2160gtgaggcttt gtaccccagc ccctgcccag gccactgtga gggtgggtgc tggctgagcc 2220cctggggcag aaggagtggg gcaggcgggg tctttgttct cggctcccac agcagagcca 2280ggtgaggggg ggcctgccag gactagacag aagtggggcg gcctgaaccc tgcttccagc 2340catggccagg ggccacggaa cccggcaggg gtgtctgagg ccgccctgtc agctggccgg 2400tccaagcctg tggctggagc tggtgtgtgt ttatctaata aagtcccaca gagtcagtct 2460<210> SEQ ID NO 25 <211> LENGTH: 745 <212> TYPE: DNA <213> ORGANISM:Homo sapiens <220> FEATURE: <221> NAME/KEY: misc_feature <223> OTHERINFORMATION: Incyte ID No: 7503563CB1 <400> SEQUENCE: 25 ctgctccctgagaacgggtc ccgcagctgg gcaggcgggc ggcctgaggg cgcggagcca 60 tgaagctgtacagcctcagc gtcctctaca aaggcgaggc caaggtggtg ctgctcaaag 120 ccgcatacgatgtgtcttcc ttcagctttt tccagagatc cagcgttcag gaattcatga 180 ccttcacgagtcaactgatt gtggagcgct catcgaaagg cactagagct tctgtcaaag 240 aacaagactatctgtgccac gtctacgtcc ggaatgatag tcttgcaggt gtggtcattg 300 ctgacaatgaatacccatcc cgggtggcct ttaccttgct ggagaaggta ctagatgaat 360 tctccaagcaagtcgacagg atagactggc cagtaggatc ccctgctaca atccattacc 420 cagccctggatggtcacctc agtagatacc agaacccacg agaagctgat cccatgacta 480 aagtgcaggccgaactagat gagaccaaaa tcattctggc ccggaaacaa aactcatgct 540 gtgccatcatgtgatgcagc ctgccagagg cccaatgctg gaatggcacc atcattcaca 600 tcagaactgcagcccctgga aaagaagaga cagccataga cgaggagcca gagtgggggc 660 agactggccatttttatttt gaagttcctg cgagaaatgg atggtggaag ggtggcgaat 720 gttcaaattcatatgtgtgg tagtg 745 <210> SEQ ID NO 26 <211> LENGTH: 2738 <212> TYPE:DNA <213> ORGANISM: Homo sapiens <220> FEATURE: <221> NAME/KEY:misc_feature <223> OTHER INFORMATION: Incyte ID No: 6244251CB1 <400>SEQUENCE: 26 gacacacaca cactgacaca catatatata aagtataaat acatattttttaaagtttat 60 ttttaaagtt ttaaagcaaa agccggcccc tcccctctcc cagagtaggcaggccccacc 120 cctctcccca agtgggtggg gacagcattt gcataggcag ctttccctgtgatgccacag 180 gttcctcggg acaaactgct gcctggccat gcctcctttc cctttcatctttctcattga 240 ccaatgggct tggagcatta aggccacacc cctattctgt gttctagtggggccctggtt 300 acgcctcctc tggctcagtc acacaggtgc ctgatacgtg actggaggtgttcgctgatg 360 tggccccaac cctgccttcc tccccacccc acgatgttag aagaaactcaacagagtaaa 420 ttggcagcag ccaagaaaaa gctaaaagaa tatcagcaga ggaacagccctggtgttcca 480 gcaggagtga agatgaaaaa gaaaaacact ggcagtagcc ctgagacagccacttttggt 540 ggttgccact cacctgggca gagtcggtac caagaactgg aattagccctggactcaagc 600 tccgcaataa tcaatcaact caatgaaaac atagaatcat tgaaacaacagaagaaacaa 660 gtggaacatc agctggaaga agtaaagaaa accaacagtg aaatacacaaagcacagatg 720 gagcagttag aggcaatcga catcctcaca ttggaaaagg cagacttgaagaccaccctt 780 taccatacta aacgtgctgc ccgacacttc gaagaagagt ccaaggatctggctggccgc 840 ctgcaatact ccttacagcg tattcaagaa ttggagcggg ctctctgtgctgtgtctaca 900 cagcagcagg aagaggacag gtcctcgagc tgcagagaag cggtcctccaccggcggtta 960 cagcagacca taaaggagcg ggcgctgctg aacgcacacg tgacacaggtgacagagtca 1020 ctaaaacaag tccagctaga gcgagacgaa tatgctaaac acataaaaggagagagggcc 1080 cggtggcagg agaggatgtg gaaaatgtcg gtggaggctc gaacattgaaggaagagaag 1140 aagcgtgaca tacatcggat acaggagctg gagaggagct tgtccgaactcaaaaaccag 1200 atggctgagc ccccatccct ggcaccccca gcagtgacct ctgtggtggaacagctacaa 1260 gatgaggcca aacacctgag gcaggaggtg gaaggtctgg agggaaagctccaatcccag 1320 gtggaaaaca atcaggcctt gagtctcctt agcaaggaac aaaagcagagactccaggag 1380 caggaggaga tgctccgaga gcaggaggcg cagagagtgc gggagcaggagagactgtgt 1440 gaacaaaacg agaggcttcg ggagcagcag aagacgctac aggagcagggtgagaggctg 1500 cgaaagcagg agcagaggct acgcaaacag gaggagaggc tgcgaaaggaggaggagagg 1560 ctgcgaaagc aggaaaagag gctgtgggac caggaggaga ggctgtgggaccaggaggag 1620 aggctgtggg agaaggagga gaggctacaa aagcaggagg agaggctcgcgctctcccag 1680 aaccacaagc tcgacaagca gctggccgag ccacagtgca gcttcgaggatctgaataac 1740 gagaacaaga gcgcactgca gttggagcag caagtaaagg agctgcaggagaggctgggc 1800 gagaaggaga cagtaacctc tgccccatcc aagaagggct gggaggtgggcaccagcctc 1860 tggggagggg agctccccac aggagatgga ggacaacatc tggacagtgaggaggaggag 1920 gcgcctcggc ccacgccaaa catcccagag gacctggaga gccgggaggccacgagcagc 1980 tttatggacc tcccgaagga gaaggcggac gggacggagc aggtggagagacgagagctt 2040 ggattcgtcc agccttctgt gatcgtgaca gacggcatga gagagtccttcaccgtatat 2100 gaaagccagg gggcagtgcc aaacacgcgg caccaggaga tggaggacttcatcaggctg 2160 gcccagaagg aggaggagat gaaggtgaag ctgctggagc tgcaagagttggtgttgccc 2220 cttgtgggcg accacgaggg gcatggcaaa ttcctcatcg ctgcccagaaccctgctgat 2280 gagcccactc caggggcccc agccccccag gaacttgggg ctgccggtgagcaggatgtt 2340 ttttatgaag tgagcctgga caacaacgtg gagcctgcac caggagcggccagggagggt 2400 tctccccatg acaaccccac tgtacagcag atcgtgcagc tgtctcctgtcatgcaggac 2460 acctaggagc acccaggctt gcccagcaaa ccctgcgtgc cattcttctaccaggcagcc 2520 gagaacaggg agataaacat catcatcttc taagagctgg tcaagaaatttaaaacaaca 2580 acaacaacaa aaagttacgg ggttcatctc ctacacaatt catttactccatttgaatgc 2640 tagagccact cacatttatt tgtgtttcta atttaccgtt taaatttatttgtaaaaagt 2700 taagggagag ttggtctttc cctgatgttc tttctggc 2738 <210> SEQID NO 27 <211> LENGTH: 2509 <212> TYPE: DNA <213> ORGANISM: Homo sapiens<220> FEATURE: <221> NAME/KEY: misc_feature <223> OTHER INFORMATION:Incyte ID No: 7503467CB1 <400> SEQUENCE: 27 ctgctggttt cattcgaggtttcgggccga ggatgccagc ccccatcaga ttgcgggagc 60 tgatccggac catccggacagcccgaaccc aagctgaaga acgagaaatg atccagaaag 120 aatgtgctgc aatccggtcatcttttagag aagaagacaa tacataccga tgtcggaatg 180 tggcaaaatt actgtatatgcacatgctgg gctaccctgc tcactttgga cagttggagt 240 gcctcaagct tattgcctctcaaaaattta cagacaaacg cattgtccca gcatttaaca 300 cggggaccat cacacaagtcattaaagttc tgaaccctca gaagcaacag ctgcgaatgc 360 ggatcaagct tacatataatcacaagggct cagcaatgca agatctagca gaggtgaaca 420 actttccccc tcagtcctggcaatgagggt ttggcaccat tctcattctt tatcccactc 480 aatcaaagga actctgggaaggaggttgtg attgctggca agtccccccc aactgtacca 540 cgggcatgag gagctgaagagaactgctga ggaggatttt cctaaagtta ctgctgacct 600 tgaagcattg ttaaagactaatgtcctctc ctccactgtt gaggctggct gcttctggag 660 gctactttgc actcttcctcttctcctttt tccgcacttc tccacccctc ccacatttac 720 agccagaatc aacattccctgggcccctga ggaaataagc agctggtctg gaggagagga 780 ctgcaatcca tggcgaaaaaacactcactt tgtctctgca gcaaagagtt gccccttctt 840 tctactgttg tttctctgtggactgggcaa ggtggggtat ttattcctca ctagctgggt 900 taccatcttc aggcacttttaacatctggc attcggaatg gaaatgtaat aatggacatt 960 agggagccct gcctttttctactggttccc ccaatgtttg aaagaggcat taggctcctg 1020 gtagcctttt ctgtgcattgctgtatacac acagacacac acatgtatgt ttgttaccaa 1080 gaactggtca gaccttgcgagtttatttgt aaacactgga cagatggagt taaaaagagc 1140 ttttgttgag atttggcatgaaggatatgg tgctctattt gtaatagaaa cttccaaggc 1200 tcttccagct cccctttctcgccattcttt agctgtagtc atgaatagtc tccatgattt 1260 tcaaaattga ttccctttaaagtgcaaaat ggtcaccttc taaaagatat attcatagtt 1320 attaatgacc ctattcccaccacaaatttt aaagtgctcc taagcccata acttgcctgt 1380 ttgaactatg gtaatgggtggaagaggagt tcaccagttt caaagatcag actctgtatc 1440 aaaagtacct ttgcccttaggaagagtgag tattggagtc atcttatcta ttactccaaa 1500 cctccctttt tatttcttgagcctggcttg gaccttggca ttccgtttga attccttcta 1560 actggaacat ttgtgttgtatctgtaacac tggcactgaa ataaagacca cacggttaaa 1620 gaaatctttc catattgtactttatggtgt tggagtgaag ccttgtagct tccatacccc 1680 tatgtcagag gaggtcttacggacaccata gggtaggaat agcctttcct cagtctgaga 1740 aattggtctc ttttaaaagacgaatctcat gaatattcac atcaaagact tgagcttttt 1800 aaactagtga gagtgccaagtgctttttag aaaggaccca tatgttatca aactttgaaa 1860 ttgagttgct ggaatgaagtagaggtgact ctctctgtgg tacacattga atgtactatg 1920 tatgttcaag tattcaggcgccatgtctta tatactgaag aaagaaaaag tgaggcccac 1980 cttgctctta caatgtttgcaattgttact gtattgaata cagtataatg actactatgg 2040 cttcaatctt aaacctggaaacaaatatcc ctttttttcc ccttcatttc accaagcctt 2100 tacttaaaat cttcagtgtcttgtcaaatc tagctctgta tcagatgctg gaatattcct 2160 aacatttgac aaactggagttgaactaaag gctccacggg aaagtttctg gtcttactag 2220 tgtgtatgag caagatctgctaaaacttac tccactgggt aaatggttga ctgagtcaag 2280 aacaggataa tatctcctgcatagttttca gtaatgtaag tgtggactag tgcatatttc 2340 agacaactgc tctgcctgtgcaatgaaaaa tagcctttaa gggtttcttt gcagactgat 2400 ttcattggat ggatacttaatgctgtgaaa catgatagga ttaacataat gttggtggat 2460 ttcttgaata gaatttgtcttaacattcaa aaaaaaaaaa aaaaaaaag 2509 <210> SEQ ID NO 28 <211> LENGTH:966 <212> TYPE: DNA <213> ORGANISM: Homo sapiens <220> FEATURE: <221>NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte ID No: 6599034CB1<400> SEQUENCE: 28 ggaagaggag ctggtgagaa gacagcgaaa tggcgcctccggcccccggc ccggcctccg 60 gcggctccgg ggaggtagac gagctgttcg acgtaaagaacgccttctac atcggcagct 120 accagcagtg cataaacgag gcgcagcggg tgaagctgtcaagcccagag agagacgtgg 180 agagggacgt cttcctgtat agagcgtacc tggcgcagaggaagttcggt gtggtcctgg 240 atgagatcaa gccctcctcg gcccctgagc tccaggccgtgcgcatgttt gctgactacc 300 tcgcccacga gagtcggagg gacagcatcg tggccgagctggaccgagag atgagcagga 360 gcgtggacgt gaccaacacc accttcctgc tcatggccgcctccatctat ctccacgacc 420 agaacccgga tgccgccctg cgtgcgctgc accagggggacagcctggag tgcacagcca 480 tgacagtgca gatcctgctg aagctggacc gcctggacctcgcccggaag gagctgaaga 540 gaatgcagga cctggacgag gatgccaccc tcacccagctcgccactgcc tgggtcagcc 600 tggccacgga tagtggctac ccggagacgc tggtcaacctcatcgtcctg tcccagcacc 660 tgggcaagcc ccctgaggtg acaaaccgat acctgtcccagctgaaggat gcccacaggt 720 cccatccctt catcaaggag taccaggcca aggagaacgactttgacagg ctggtgctac 780 agtacgctcc cagcgcctga ggctggccca gagctgtcaggaccatgaag ccaggacaga 840 ggccaggagc cagccctgca gccctcccca cccggcatccacctgcatcc cctctggggc 900 aggagcccac ccccagcacc cccatctgtt aataaatatctcaactccag gtgtccacct 960 gaaaaa 966 <210> SEQ ID NO 29 <211> LENGTH:820 <212> TYPE: DNA <213> ORGANISM: Homo sapiens <220> FEATURE: <221>NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte ID No: 7504179CB1<400> SEQUENCE: 29 ctcgtttggt aggaaaagga ctggctctga ctcttcacccatcttcaccc aggctggccc 60 ctttggtgaa actacaactc ccaggggtct gtgcgcgagaaggcaggcgg gtttttctac 120 cggaagtccg ctctagctct gggccctaca actgcaccctgagccggagc tgcccagtcg 180 ccgcgggacc ggggccgctg gggtctggac gggggtcgccatgttccgga actttaagat 240 catttaccgc cgctatgctg gcctctactt ctgcatctgtgtggatgtca atgacaacaa 300 cctggcttac ctggaggcca ttcacaactt cgtggaggtcttaaacgaat atttccacaa 360 tgtctgtgaa ctggacctgg tgttcaactt ctacaaggtttacacggtcg tggacgagat 420 gttcctggct ggcgaaatcc gagagaccag ccagacgaaggtgctgaaac agctgctgat 480 gctacagtcc ctggagtgag ggcaggcgag ccccaccccggccccggccc ctcctggact 540 cgcctgctcg cttccccttc ccaggcccgt ggccaacccagcagtccttc cctcagctgc 600 ctaggaggaa gggacccagc tgggtctggg ccacaagggaggagactgca ccccactgcc 660 tctgggccct ggctgtgggc agaggccacc gtgtgtgtcccgagtaaccg tgccgttgtc 720 gtgtgatgcc ataagcgtct gtgcgtggag tccccaataaacctgtggtc ctgcctggca 780 aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa820 <210> SEQ ID NO 30 <211> LENGTH: 3709 <212> TYPE: DNA <213>ORGANISM: Homo sapiens <220> FEATURE: <221> NAME/KEY: misc_feature <223>OTHER INFORMATION: Incyte ID No: 71249354CB1 <220> FEATURE: <221>NAME/KEY: unsure <222> LOCATION: 3647, 3652 <223> OTHER INFORMATION: a,t, c, g, or other <400> SEQUENCE: 30 cggaggagcc tggcgccgcc attttcctgcagctgcctgt tcctcttacc ctgcccggct 60 ccagctgacc agggaagggg tgggctgaactgaggcgggg gcaagggagt gcccgacatc 120 ttgtccgact ccgcgggtga cacgagccggttctctctgg actggtggca gcgcgcggcc 180 ccgaaccgcg ccccaggccg gcaggcggggaaggagccgg tgggggtagg gggtgcggtg 240 gggggtgggg accctccggc tcttgggggtcccagtcccc gccggctgct gagcgggtgg 300 ggtggtggag gagctgcaga gatgtccggccagagcctga cggaccgaat cactgccgcc 360 cagcacagtg tcaccggctc tgccgtatccaagacagtat gcaaggccac gacccacgag 420 atcatggggc ccaagaaaaa gcacctggactacttaattc agtgcacaaa tgagatgaat 480 gtgaacatcc cacagttggc agacagtttatttgaaagaa ctactaatag tagttgggtg 540 gtggtcttca aatctctcat tacaactcatcatttgatgg tgtatggaaa tgagcgtttt 600 attcagtatt tggcttcaag aaacacgttgtttaacttaa gcaatttttt ggataaaagt 660 ggattgcaag gatatgacat gtctacatttattaggcggt atagtagata tttaaatgag 720 aaagcagttt catacagaca agttgcatttgatttcacaa aagtgaagag aggggctgat 780 ggagttatga gaacaatgaa cacagaaaaactcctaaaaa ctgtaccaat tattcagaat 840 caaatggatg cacttcttga ttttaatgttaatagcaatg aacttacaaa tggggtaata 900 aatgctgcct tcatgctcct gttcaaagatgccattagac tgtttgcagc atacaatgaa 960 ggaattatta atttgttgga aaaatattttgatatgaaaa agaaccaatg caaagaaggt 1020 cttgacatct ataagaagtt cctaactaggatgacaagaa tctcagagtt cctcaaagtt 1080 gcagagcaag ttggaattga cagaggtgatataccagacc tttcacaggc ccctagcagt 1140 cttcttgatg ctttggaaca acatttagcttccttggaag gaaagaaaat caaagattct 1200 acagctgcaa gcagggcaac tacactttccaatgcagtgt cttccctggc aagcactggt 1260 ctatctctga ccaaagtgga tgaaagggaaaagcaggcag cattagagga agaacaggca 1320 cgtttgaaag ctttaaagga acagcgcctaaaagaacttg caaagaaacc tcatacctct 1380 ttaacaactg cagcctctcc tgtatccacctcagcaggag ggataatgac tgcaccagcc 1440 attgacatat tttctacccc tagttcttctaacagcacat caaagctgcc caatgatctg 1500 cttgatttgc agcagccaac ttttcacccatctgtacatc ctatgtcaac tgcttctcag 1560 gtagcaagta catggggagg attcactccttctccagttg cacagccaca cccttcagct 1620 ggccttaatg ttgactttga atctgtgtttggaaataaat ctacaaatgt tattgtagat 1680 tctgggggct ttgatgaact aggtggacttctcaaaccaa cagtggcctc tcagaaccag 1740 aaccttcctg ttgccaaact cccacctagcaagttagtat ctgatgactt ggattcatct 1800 ttagccaacc ttgtgggcaa tcttggcatcggaaatggaa ccactaagaa tgatgtaaat 1860 tggagtcaac caggtgaaaa gaagttaactgggggatcta actggcaacc aaaggttgca 1920 ccaacaaccg cttggaatgc ggcaacaatgaatggcatgc attttccaca atacgcaccc 1980 cctgtaatgg cctatcctgc tactacaccaacaggcatga taggatatgg aattcctcca 2040 caaatgggaa gtgttcctgt aatgacgcaaccaaccttaa tatacagcca gcctgtcatg 2100 agacctccaa acccctttgg ccctgtatcaggagcacaga tacagtttat gtaacttgat 2160 ggaagaaaat ggaattactc caaaaagacaagtgctcaag cagcaaaatc cttacttcca 2220 gcaaaatcca aactgctgtc tcttaaatctcttaaactct cttcttccat tagaatgcta 2280 caagtaactc agtgaaggcc catgaaggaaattgggacta gtttatagga gaacgtatca 2340 atacagttta taaagccaag aattgctatgatttaagact aagatctgtc tttttggtga 2400 ctaacccttc aattctttca actcctgttaatacccataa tcagtaacct atcaagaaaa 2460 gcccttattt ggaaagtgtg aaatttgtatttggaaaagc tgcctggaga gaagaactgt 2520 gtcctttact gtatttcaac aggactcttttgggggatca aaattaaaat tcctaattat 2580 gcattatctt tcttttctcc agtcctcacaaatacagaaa caataactga aattaacttt 2640 tcttttttta aaaaaaatta tattcagtttgcagtagaca ttccttaagt atttgtattt 2700 atttatgatt atcaatttta cataacattaatattgtatc agacctcctt atgaaaatga 2760 gtatggatgt gcacagtatg tttgatttttatccacaaga atgaatctga ttcagaatgc 2820 ttttctcagc tgacatacag agcactaaatattttaaggc aagtccatag gtctgaatct 2880 cttaagaatt ctcggcctct gtgggatttagggaagcatt ataaatgcat taatccttat 2940 agtcaattct gtgcctagga ttttgccagggaacagttca ctgactagga aaagcactac 3000 attttaaatt cagcattagt gcattgggaaggatctttac tgctttgtgc ttggcatgtc 3060 attattttcc atttgacatt agggcctttccaaaatgaat gtgaggaatt gctttcactt 3120 caagactttc cttcttttca ctaaaactctagaaggtgtt acaaggggga gggaaggggg 3180 gcaaagtcct tgaacatttt ctttggctcgtgccatgtta tgatcatata ccttttaaat 3240 aaggggaaat agtatcttta aagttaatgtctagccaaga gtttagtaaa cgaagaatta 3300 aactgcactg ttgatcggtg ctttgtgtaaatacatcttt aacatttggg tggagagggg 3360 ccttaagaag gacagttcat tgtaggaaagcaattctgta catgagttta agcattcttg 3420 ttgcattgtc tctgcagatt ctatttttgtttacaatatt aaaatgtatg ttagcaaaat 3480 gggtggattt tcaaataaaa tgcagcttccacaaaagttt tgttatggta ttctggtctg 3540 agatgcattt tcatttttcc tttctctttttattatcaat attgtcattt ttccctaata 3600 aaatataccc aggtgattat atttgttgatctaataacat ggaaggnttg tnttatatga 3660 attttccaaa agatgtctct ttacactttttgttaccttg taagactcc 3709 <210> SEQ ID NO 31 <211> LENGTH: 461 <212>TYPE: DNA <213> ORGANISM: Homo sapiens <220> FEATURE: <221> NAME/KEY:misc_feature <223> OTHER INFORMATION: Incyte ID No: 7505803CB1 <220>FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 325 <223> OTHERINFORMATION: a, t, c, g, or other <400> SEQUENCE: 31 cgcggtcggtcttgtgggct gaggggcagc ggcttaggct ccggcgtctg caggggtcgc 60 cgagctaacccgtggctagg cgagtggggc ggggcggccg gcaccatgtc gaggcaggcg 120 aaccgtggcaccgagagcaa gaaaatggtc cagatggctg tggaggccaa gtttgtccag 180 gacaccctgaaaggagacgg tgtgacagaa atccggatga gattcatcag gcggattgag 240 gacaatcttccagctggaga ggaataacca tccctacaac tcgaggatag ccatcaggag 300 cactgttggaatcagcaggc ctctntgctc cctctgccct ccagaactca gtgactcttg 360 aacatggatgttatatattc ttataacctg tttccattct ccattcaaat aaagagcaga 420 ctgcgatatagtccatttaa aaaaaaaaaa aaaaaaaaaa a 461 <210> SEQ ID NO 32 <211> LENGTH:1254 <212> TYPE: DNA <213> ORGANISM: Homo sapiens <220> FEATURE: <221>NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte ID No: 7505804CB1<400> SEQUENCE: 32 ggctgttgct gtggtttcct gagttgctgc tgctgcggcggcggcagcgg cgtctgtgct 60 tgtggaggtg tcggcctctg ggcggatgtt gacattgtgttgttgttatt gctgatggta 120 atggcggcgg cggtggcggc gacggtccag accccatcccctctgtagcc ggagccgaga 180 cagccgacag cgaactccgc ggcctcggag ccggcggcagcggcgactcc cctcagcctc 240 cgccgcctcg cccgccggta ccccggcgcc aaccccgggagtcaggccct ttgggcaggg 300 gagctcggag gctcaggatg gcggatttcg acgaaatctatgaggaagag gaggacgagg 360 agcgggccct ggaggagcag ctgctcaagt actcgccggacccggtggtc gtccgcggct 420 ccggtcacgt caccgtattt ggactgagca acaaatttgaatctgaattc ccttcttcat 480 taactggaaa agtagctcct gaagaattta aagccagcatcaacagagtt aacagttgtc 540 ttaagaagaa ccttcctgtt aatacacgaa gatcgattgagaagttatta gaatgggaaa 600 acaataggtt ataccacaag ctgtgcttgc attggagactgagcaaaagg aaatgtgaaa 660 cgaataacat gatggaatat gtcatcctca tagaatttttaccaaagaca ccgatttttc 720 gaccagatta gcatttactt tatttataga gactttccaagtatgttgtc tttccaatgg 780 tgccttgctt ggtgctctcc tggtggtgac ataacattggttctacagaa tcgtgtggtg 840 ttttttttgt ttttgttttt tttttttttt taaataaccgcatgttctaa gtgtgcattt 900 ttgtcaatct ttgcaacagt tatttcatac agatgtttaatacttaagtt attgtgctct 960 tttctgttat gtattctgat tttcaaggat tacttttttgtattatcaaa aaaatacatt 1020 tgaacttagc ataaaaagtg gccagccttt tttattttgtcaccaaggta cacacagtcc 1080 tttatttata aattccttaa cagagaaaaa cacctttgtaaggctcaact tacctattcc 1140 agcaagcaca ctttttctgt cattttttct ttcttttcaaatttgatatt gtcattattt 1200 taaaatagta agtgttcttt aatagtcttt tgggacctaacatacccttt ctca 1254 <210> SEQ ID NO 33 <211> LENGTH: 1176 <212> TYPE:DNA <213> ORGANISM: Homo sapiens <220> FEATURE: <221> NAME/KEY:misc_feature <223> OTHER INFORMATION: Incyte ID No: 7505846CB1 <400>SEQUENCE: 33 ccggaaagct ccgaggagga gcctggcgcc gccattttcc tgcagctgcctgttcctctt 60 accctgcccg gctccagctg accagggaag gggtgggctg aactgaggcgggggcaaggg 120 agtgcccgac atcttgtccg actccgcggg tgacacgagc cggttctctctggactggtg 180 gcagcgcgcg gccccgaacc gcgccccagg ccggcaggcg gggaaggagccggtgggggt 240 agggggtgcg gtggggggtg gggaccctcc ggctcttggg ggtcccagtccccgccggct 300 gctgagcggg tggggtggtg gaggagctgc agagatgtcc ggccagagcctgacggaccg 360 aatcactgcc gcccagcaca gtgtcaccgg ctctgccgta tccaagacagtatgcaaggc 420 cacgacccac gagatcatgg ggcccaagaa aaagcacctg gactacttaattcagtgcac 480 aaatgagatg aatgtgaaca tcccacagtt ggcagacagt ttatttgaaagaactactaa 540 tagtagttgg gtggtggtct tcaaatctct cattacaact catcatttgatggtgtatgg 600 aaatgagcct ccacaaatgg gaagtgttcc tgtaatgacg caaccaaccttaatatacag 660 ccagcctgtc atgagacctc caaacccctt tggccctgta tcaggagcacagatacagtt 720 tatgtaactt gatggaagaa aatggaatta ctccaaaaag acaagtgctcaagcagcaaa 780 atccttactt ccagcaaaat ccaaactgct gtctcttaaa tctcttaaactctcttcttc 840 cattagaatg ctacaagtaa ctcagtgaag gcccatgaag gaaattgggactagtttata 900 ggagaacgta tcaatacagt ttataaagcc aagaattgct atgatttaagactaagatct 960 gtctttttgg tgactaaccc ttcaattctt tcaactcctg ttaatacccataatcagtaa 1020 ccctatcaag aaaagccctt atttggaaag tgtgaaattt gtatttggaaaagctgcctg 1080 gagagaagaa ctgtgccctt tactgtattt caacaggact cttttgggggatcaaaatta 1140 aaattcctaa ttatgcatta tctttctttt ctccag 1176 <210> SEQID NO 34 <211> LENGTH: 9050 <212> TYPE: DNA <213> ORGANISM: Homo sapiens<220> FEATURE: <221> NAME/KEY: misc_feature <223> OTHER INFORMATION:Incyte ID No: 55004585CB1 <400> SEQUENCE: 34 gcggccggga gcagcttcagtgggcacacg acagccgcgc gacccgtggc ggggcgagct 60 gtggcagtag catcctcaccactcgcagca gcctcagccg cggcgcccgt agcgccagca 120 gcggctgctt ttgcaaaggctgagcgcagg ggcggggcgg gccaggaagc catggagttc 180 tgtgcagccg cggactcccggggagcggac tagggaaact tggaggctgc gaccagggtt 240 tggcgttgtt gtcagcctcggggagagaga ttggacaaat attctccaag aggaggaggg 300 cgacgccaag gactttccacatcaactgct ttggggtatc tccacaagtt ggaagaggga 360 ccctttcgtt ttgcattgcgtgtgttgtgc tcattaccag tgcagcgact gccgtcccag 420 ggtgactctg agttgtcctttatcgtgagc tagcaatggc tagcgaagac aatcgtgtcc 480 cttccccgcc accaacaggtgatgacgggg gaggtggagg gagagaagaa acccctactg 540 aagggggtgc attgtctctgaaaccagggc tccccatcag gggcatcaga atgaaatttg 600 ccgtgttgac cggtttggttgaagttggag aagtatccaa tagggatatt gtagaaactg 660 tctttaacct gttggtaggaggacagtttg atctggaaat gaatttcatt atccaagaag 720 gtgagagtat taactgcatggtggacctac tggaaaaatg tgacattacg tgccaagcag 780 aagtctggag catgtttacagccattctga agaaaagcat acggaatctt caagtctgca 840 ctgaagtagg ccttgttgaaaaagtgcttg ggaaaattga aaaagttgac aatatgatag 900 cagatctttt ggttgacatgttgggagtgc tggctagcta taatttgaca gttcgcgagc 960 taaagctttt cttcagtaaacttcaaggag ataaaggacg atggcctcca catgctggga 1020 agttgctgtc tgtgttaaagcatatgcctc agaagtatgg tcctgatgcc ttttttaact 1080 ttccaggaaa gagtgctgcagctattgcat tacctcctat agccaaatgg ccataccaga 1140 atggttttac atttcatacatggcttagaa tggatcctgt aaataacatc aatgtagata 1200 aggataaacc atatttgtattgtttcagaa ccagcaaagg tcttggctat tctgctcatt 1260 ttgttggagg ctgtttgattgtaacatcaa taaagtcaaa aggaaaaggc tttcaacact 1320 gtgtgaaatt tgatttcaagccacaaaagt ggtatatggt taccatagta cacatctata 1380 accgatggaa gaatagtgaacttcgatgtt atgtgaatgg tgagctggct tcctatggag 1440 agataacatg gtttgtcaacactagcgata cctttgacaa atgtttcctg ggctcatcag 1500 aaacagcaga tgctaatagagtattctgtg gtcagatgac tgcagtttac cttttcagtg 1560 aagctctaaa tgcagctcagatatttgcta tttatcagtt gggcctggga tacaagggta 1620 catttaaatt caaagcagaaagcgaccttt tccttgctga gcatcacaaa cttttattgt 1680 acgatgggaa actctctagtgccattgcat tcacgtacaa tccacgggct acagatgccc 1740 agctttgtct tgaatcatctcctaaggaca acccttcaat ttttgttcat tcaccacatg 1800 cactcatgct ccaggatgtaaaggcagttt taacacattc catccaaagt gcaatgcatt 1860 caattggagg agtacaagtactatttccac tttatgcaca gttggattac aggcaatatt 1920 tgtctgatga gactgagttgactatatgtt caaccttgct ggcctttatc atggaatcgt 1980 tgaagaactc aattgctatgcaggaacaga tgcttgcctg taagggcttc ttggtaatag 2040 gatatagcct tgaaaagtcttccaaatctc atgttagcag agcagtactt gaactttgcc 2100 ttgcattttc aaaatatctgagtaatctgc agaatgggat gcccctgctc aagcaattgt 2160 gtgatcacgt tcttcttaatcctgccatat ggattcatac cccagccaag gttcaactga 2220 tgctctatac tgatctgtccacggaattca ttggtacagt caacatatat aacaccattc 2280 ggagagttgg aacagtgcttctcatcatgc acacgctgaa gtactactac tgggcagtga 2340 atcctcagga tcgaagtggtatcaccccaa aaggattaga tggaccgcga cctaatcaaa 2400 aagaaatgct ttctctacgagcattcttgt tgatgttcat taagcaatta gtgatgaagg 2460 attctggagt aaaggaagatgaattacagg ccattcttaa ttacctactg actatgcatg 2520 aggatgacaa tctaatggatgtcctacagc tgcttgttgc attaatgtca gaacacccta 2580 actctatgat tcctgcttttgaccaaagga atgggttacg tgttatctac aaacttctgg 2640 catcgaaaag tgaaggaatcagggtacaag ctcttaaggc aatgggttat tttttaaaac 2700 atctggcccc aaagaggaaagcagaagtca tgcttggaca tggattgttt tcattgctag 2760 ctgaaaggct catgcttcagacaaatttaa tcacaatgac cacatataat gtgctgtttg 2820 agattcttat agaacagattggtactcagg tgatacataa acagcatcca gatcctgatt 2880 cttcagtgaa gatacaaaaccctcagatac taaaagtaat tgcgacccta cttcgaaatt 2940 ctccccagtg cccagagagcatggaggttc gcagagcctt tctttctgac atgattaaac 3000 tttttaataa cagtagagaaaacaggagga gcttgctaca atgctctgtg tggcaagaat 3060 ggatgctttc tctctgctattttaatccta agaattcaga tgagcaaaag ataacagaaa 3120 tggtatacgc catattcagaatcctgcttt accatgcagt caaatatgag tggggtggct 3180 ggcgtgtatg ggtagacactttatcaatca ctcattcaaa ggtcactttt gaaatacaca 3240 aagaaaacct tgccaatatatttagggaac agcaaggaaa agttgatgaa gaaatagggc 3300 tgtgttcttc aacttcagttcaagcagcct ctggcattag aagggatatt aatgtttcag 3360 taggatccca gcaaccagatacgaaggatt ctcctgtctg tcctcatttc accacaaatg 3420 gtaatgaaaa ttcaagtatagagaagacaa gttcactaga atctgcatct aatattgaac 3480 tgcaaactac taatacatcttatgaagaaa tgaaagctga gcaagaaaat caggagttac 3540 cagatgaagg cactttggaagaaacactga caaatgagac aaggaatgca gatgatttag 3600 aagtatcttc tgacataatagaagctgtgg ctatttcctc taattctttt ataacaactg 3660 gcaaagattc aatgactgtcagtgaagtaa ctgcttctat aagttctcct tcagaagagg 3720 atggctcaga gatgccagaattcttggata aatctatagt agaggaagag gaagatgatg 3780 attatgtgga actgaaagtagaaggcagtc ctactgagga agctaatcta cccacagagc 3840 tccaagataa cagtttgtctccagctgcat ctgaagccgg tgaaaagctg gacatgtttg 3900 gtaatgatga caaattaatatttcaagaag gaaaacctgt tactgaaaag caaactgata 3960 ctgaaactca agattctaaagattctggaa ttcagactat gacagcatca gggtcttcag 4020 ctatgtcacc agaaactactgtttcccaaa tagctgtaga atcagacctt ggtcagatgc 4080 tggaggaagg gaagaaagcaactaacctca ctagagaaac caaattaatt aatgattgtc 4140 atggtagtgt ctctgaggcttcttctgagc aaaagattgc gaagttggat gtttccaatg 4200 ttgctacaga tactgagaggctggagttga aggccagtcc caacgtggaa gcacctcaac 4260 ctcatcgaca tgtgcttgagatatcaaggc aacatgagca gccagggcaa ggaatagcac 4320 cagatgcagt taatggacaaaggagggatt ccagatctac tgtgtttcgt attcctgagt 4380 tcaactggtc tcagatgcatcaacgtttgc tcactgatct attattttca atagaaacag 4440 atatacagat gtggagaagccattcaacaa agacagttat ggacttcgtg aatagcagtg 4500 ataatgtcat ctttgtacacaacacaattc atctcatctc tcaagtgatg gacaatatgg 4560 tcatggcttg tgggggtatactgccattgc tttcagctgc tacatcggct acacatgaac 4620 tggaaaatat tgaacctactcaaggccttt caatagaagc ctctgtgaca tttttgcaga 4680 ggctaattag ccttgtggatgtgcttatat ttgcaagttc tcttggcttt actgaaattg 4740 aagctgaaaa aagtatgtcatctggaggaa ttttgcggca gtgtctccga ctagtttgtg 4800 cagtcgcagt aaggaattgcttggagtgtc aacagcattc acaactgaaa actaggggag 4860 ataaagcctt gaaaccaatgcatagcctta ttcctttagg gaaatctgca gcgaagagcc 4920 cagtggacat tgtgactggcggtatatctc cagtaagaga tcttgacagg cttctacagg 4980 acatggatat taatcggcttagggcagttg ttttcagaga catagaggat agcaaacaag 5040 ctcaattttt agccttggcagtagtatact ttatctctgt tcttatggtc tccaagtaca 5100 gagacatttt ggaaccccaaaatgaaaggc atagccagtc atgtacagaa actggcagtg 5160 aaaatgagaa tgtatcactctctgaaatca caccagcagc attcagcact ttaactacgg 5220 catcagtgga agaatctgaaagcacatcat ctgctcgaag gagggactca ggcattgggg 5280 aagaaacagc cactggtttaggaagccatg tggaagtaac tcctcacaca gcacctcctg 5340 gtgtcagtgc aggcccagatgcaatcagcg aggtgctatc tactctttct ttagaagtca 5400 ataagtctcc ggaaaccaaaaatgatagag gaaatgactt ggacactaag gctacaccgt 5460 cagtttcagt ttcaaaaaacgtcaatgtga aagacattct ccgaagcttg gttaacatac 5520 cagcagatgg agtcacagtggatcctgccc ttctgccacc agcctgcctt ggagcccttg 5580 gtgatctatc tgtggaacaacccgtgcagt tcagatcttt tgacagaagt gtcattgttg 5640 cagcaaaaaa gtcagcagtctcaccttcca cctttaatac aagcatacct accaatgctg 5700 tcagtgtggt ttcctcagtagattcagccc aagcctcaga tatgggagga gaatcaccag 5760 gcagtagatc atctaatgcaaaattgccct cagttccaac agttgattca gtttcacaag 5820 atccggtttc aaatatgagtattacagaga ggcttgaaca cgctttggaa aaggcagctc 5880 ctctccttcg tgagatttttgtggattttg caccttttct ttctcggaca cttttgggta 5940 gccatggaca agaactgcttatagaaggaa caagtctggt ttgcatgaag tcgagtagtt 6000 cagttgtgga attggttatgctactgtgtt ctcaggagtg gcaaaattct attcagaaga 6060 atgcaggcct tgcttttatcgaacttgtca atgaaggaag gttgcttagc cagacaatga 6120 aggatcatct agtaagagtagcaaatgaag ctgaatttat cctgagcagg cagagagcag 6180 aagatattca cagacatgcggaatttgagt cactgtgtgc ccagtattct gcagacaaac 6240 gagaagatga gaagatgtgtgatcatttga taagagcagc aaaatatcgt gaccacgtga 6300 cagcaactca actaatccagaaaattatca acattctcac agacaagcat ggagcctggg 6360 gaaattctgc agtgagtcgtcctcttgagt tctggcgcct tgactactgg gaagatgact 6420 tgcggcgccg gcgacgatttgtgcgtaacc ctctaggatc gacacatcct gaagcgacac 6480 taaaaacagc cgtggaacatgccacagatg aagatatcct tgctaaagga aaacagtcca 6540 tcaggagtca ggctttaggaaatcagaact cagaaaacga gatcctcctg gaaggcgatg 6600 atgatactct gtcatccgtggatgagaaag atttagagaa tcttgccggt cctgttagcc 6660 tgagcacacc agctcagcttgtggccccct ctgttgtagt aaagggcact ctttctgtca 6720 cctcctccga actctattttgaggtggatg aagaggatcc taacttcaaa aaaatcgacc 6780 ccaagatctt ggcatatacagaagggctgc atggaaaatg gctgttcaca gagatacgat 6840 caatcttttc tcgtcgttatcttttgcaaa atacagccct ggagatcttt atggcaaaca 6900 gagttgctgt gatgttcaacttcccagacc ctgcaacagt aaagaaagtg gttaactatc 6960 tacctcgtgt tggcgttggaacaagttttg gattgcctca aaccagacgt atttcattag 7020 ctagtccacg tcagctttttaaggcttcta atatgaccca gcgatggcaa cacagagaga 7080 tatctaattt tgagtacttgatgtttctca acacgatagc aggacggagt tataatgact 7140 taaatcagta tccagtgtttccttgggtca tcactaatta tgaatcagaa gaactggatc 7200 ttaccttgcc caccaacttcagagatttgt ccaagccaat aggagctctg aacccaaaaa 7260 gagcagcatt cttcgctgagcgttatgaat catgggaaga tgatcaagtt ccaaagtttc 7320 actatggtac tcattactcaactgcaagtt ttgttcttgc atggctgcta agaatagaac 7380 cctttacaac ttatttcctaaatttgcaag gaggcaaatt tgatcatgca gatcgaactt 7440 tttcatcaat ttccagagcttggcgaaaca gtcagcgtga tacctctgat attaaggagt 7500 tgatccctga attttattatctccctgaga tgtttgtcaa cttcaataat tataatcttg 7560 gagtgatgga tgatgggacagtagtgtctg atgtcgaact tcctccttgg gccaaaacct 7620 cagaagaatt tgttcacataaacagattgg ccctggagag tgaatttgtt tcctgccagc 7680 ttcaccaatg gattgatctcatttttggct ataaacagca aggaccagaa gctgtccgag 7740 ccctcaatgt gttctattacttgacctatg aaggagctgt caatctgaat tcaataactg 7800 atcctgtgtt gagagaggctgttgaagctc aaatccgaag ttttggacag actccttctc 7860 aactactcat agagccccatcctcccagag gttctgccat gcaagtgagt ccattgatgt 7920 tcacagacaa agcccagcaggatgttatca tggtcctcaa gtttccctcc aactcccctg 7980 ttactcacgt ggcagccaacacccagcctg gtttggcaac tcccgctgtg atcacagtca 8040 ctgctaacag gttatttgcggtgaacaaat ggcacaacct tcctgctcat caaggtgctg 8100 tacaagacca gccataccagctgccagtgg aaatcgatcc tctcatagcc agcaatacag 8160 gaatgcacag gaggcaaatcactgaccttt tagaccaaag tattcaagtg cattcccagt 8220 gctttgtcat cacttcagacaaccgctata ttctcgtctg tggcttctgg gataaaagtt 8280 tcagagtcta ttctacagacacaggaagat tgatccaagt ggtgtttggc cattgggatg 8340 tcgtcacttg ccttgctcgttctgagtcat atattggggg aaattgctac attctctcag 8400 ggtcacgtga tgcaactcttttgctgtggt attggaatgg aaaatgcagt gggattggag 8460 ataacccagg cagtgagactgctgctcctc gggccatttt gaccggccat gactatgagg 8520 tcacatgtgc tgcggtgtgtgcggagctag gcctggtgtt gagtggttca caagaaggac 8580 catgtctcat acattccatgaatggagact tgttgaggac cttggagggt cctgaaaact 8640 gcctgaaacc aaaactcattcaggcttcaa gagagggtca ttgtgtcata ttctatgaaa 8700 acggcctctt ctgtacattcagtgtgaatg gaaaactcca ggccacgatg gaaacagatg 8760 ataacataag agccatccagctgagccgag atgggcagta cctgctcaca ggaggagaca 8820 gaggagtggt cgtggtccggcaggtgttgg acctcaagca gctctttgcc tatccaggat 8880 gtgacgctgg aatccgggccatggcgctgt cttacgacca gaggtgcatc atttctggca 8940 tggcttcagg aagcattgtgctattttaca acgactttaa ccggtggcat catgaatacc 9000 aaacccgcta ctgatggtgacagctgtaca tcaactctgc ccctagatga 9050 <210> SEQ ID NO 35 <211> LENGTH:1605 <212> TYPE: DNA <213> ORGANISM: Homo sapiens <220> FEATURE: <221>NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte ID No: 7506012CB1<400> SEQUENCE: 35 ggcgccgggt ttcccgcggt ccgagctggc gcgggcggaggagaatcgct cttaaagggc 60 cagcgcacac gcgttctttt gttccggggc cgcagggcggggcaggcccg actttcgccg 120 tcttcttgtc tactctccag aacggccatg atttcccaattcttcattct gtcctccaag 180 ggggacccgc tcatctacaa agacttccgc ggggacagtggcggccggga tgtggccgag 240 ctcttctacc ggaagctgac gggactgcca ggagacgagtccccggttgt catggactat 300 ggctatgtac agaccacatc cacggagatg ctgaggaatttcatccagac ggaagctgtg 360 gtcagcaagc ccttcagcct ctttgacctc agcagcgttggcttgtttgg ggctgagaca 420 caacagagca aagtggcccc cagcagtgca gccagccgccccgtcctgtc cagtcgctct 480 gaccagagcc aaaagaatga agtttttttg gatgtggtcgagagattgtc tgtactgata 540 gcatctaatg gatccctgct gaaggtggat gtgcagggagagattcggct caagagcttc 600 cttcctagcg gctctgagat gcgcattggc ttgacggaagagttttgtgt ggggaagtca 660 gagctgagag gttatgggcc aggaatccgg gtcgatgaagtctcgtttca cagctctgtg 720 aatctggacg aatttgagtc tcatcgaatc ctccgcttgcaaccacctca gggcgagctg 780 actgtgatgc ggtaccaact ctccgatgac ctcccctcaccgctcccctt ccggctcttc 840 ccctctgtgc agtgggaccg aggctcaggc cggctccaggtttatctaaa gttgcgatgt 900 gacctgctct caaagagcca agccctcaat gtcaggctgcacctccccct gcctcgaggg 960 gtggtcagcc tgtctcagga gctgagcagc ccagagcagaaggctgagct ggcagaggga 1020 gcccttcgct gggacctgcc tcgggtgcaa ggaggctctcaactctcagg ccttttccag 1080 atggacgtcc cagggccccc aggacctccc agccatgggctctccacctc ggcctctcct 1140 ctggggctgg gccctgccag tctctccttc gagcttccccggcacacgtg ctctggcctc 1200 caggtccgat tcctcaggct ggccttcagg ccatgcggcaatgccaaccc ccacaagtgg 1260 gtgcgacacc taagccacag cgacgcctat gtcattcggatctgaggctc cccaaacgag 1320 gacacgacgg ccaaggtggc agtttgtccc acgggaggacagtcgtttct tttccagcct 1380 cctggccttc ggactctgaa tctgggcagg aagagtcctcagtcccaaga ccaggagggg 1440 gcaatgggcc cagcctttct gtggtatctg atgcaggaaggactgcagtg gatcagaact 1500 tacaaaccaa acttttattc tgagaaactg gctgtacaatatctaaaaag aaagtgacat 1560 gaaggaagca atctacaact tccttccgct tagcgagcaaaaaaa 1605 <210> SEQ ID NO 36 <211> LENGTH: 5038 <212> TYPE: DNA <213>ORGANISM: Homo sapiens <220> FEATURE: <221> NAME/KEY: misc_feature <223>OTHER INFORMATION: Incyte ID No: 7506212CB1 <400> SEQUENCE: 36ctgacagctg ctgataaggt ggcggcggcg aaggcagcgg caggtcggga gcaagatggc 60gctgcggcca ggagctggtt ctggtggcgg cggggccgcg ggagctggcg cggggtccgc 120cgggggaggc ggcttcatgt ttcctgttgc aggtgggata agaccccctc aaggaggcct 180gatgccgatg cagcaacaag gatttcctat ggtctctgtc atgcagccta atatgcaagg 240cattatggga atgaattaca gctctcagat gtcccaagga cctattgcta tgcaggcagg 300aataccaatg ggaccaatgc cagcagcggg aatgccttac ctaggacaag cacccttcct 360gggcatgcgt cctccaggcc cacagtacac tccagacatg cagaagcagt ttgccgaaga 420gcagcagaaa cgatttgaac agcagcaaaa actcttagaa gaagaaaaaa aaagacgcca 480gtttgaagag cagaagcaaa agctcagact tttgagcagt gtgaaaccca agacaggaga 540gaagagtaga gatgatgctt tggaagccat aaaaggaaat ttagatgggt tttccagaga 600tgcaaaaatg caccctactc cagcatcgca ccccaagaaa ccaggccctt ccttggagga 660gaagttccta gtatcttgtg atataagtac atctgggcag gaacaaatta aattaaatac 720ttctgaagtt ggccacaaag ccctaggccc aggttccagt aagaagtatc ccagtttaat 780ggccagtaac ggggttgctg tagatggatg tgtaagtggt accaccactg cagaggcaga 840aaatacttca gatcaaaacc tgtcaattga agagagtggt gtgggagtat ttccctcaca 900ggatcctgct cagcccagaa tgcctccttg gatttacaat gagagtttgg ttccagatgc 960ctataagaaa atcttagaaa ccacaatgac tccaactgga atagatactg ccaaactgta 1020tcccattctg atgtcatctg ggcttcccag ggaaactctt ggacagatat gggccttagc 1080taatcgaact acacctggca aacttacaaa agaagaactt tataccgttc tagccatgat 1140agcggtaaca cagaagggcg ttcctgcaat gagtcctgat gctttaaacc agttcccagc 1200agctcctatt ccaactttaa gtggcttttc tatgactctg cctacaccgg tgagtcagcc 1260aactgtgata ccttcaggtc ctgcgggctc catgcccctc agccttggac agccagtcat 1320gggcattaac cttgttggac cagtgggtgg agctgcagcc caggcttcta gtggtttcat 1380accaacctac cctgcaaatc aggtagtaaa gccagaagaa gatgacttcc aggattttca 1440agatgcttct aagtcaggat cccttgatga ctcattcagt gatttccaag agttgcctgc 1500ttcttcaaaa acaagtaact cccagcatgg aaacagtgcc ccttctttgt tgatgccact 1560tcctggaact aaagcattgc cttcaatgga caaatatgct gtgtttaaag gaattgcagc 1620tgacaagtcc tctgaaaata ctgttccacc tggagatcct ggtgataaat atagtgcttt 1680cagagaactt gaacagacag cagagaataa acctttagga gaaagctttg cagaattcag 1740atctgcagga actgatgatg gtttcaccga ttttaaaaca gccgatagtg tatcaccact 1800agagccacca acaaaagaca aaacttttcc accatccttc ccctcaggaa ctatacaaca 1860gaaacaacaa acacaagtga aaaaccctct gaacttagca gacctagata tgttttcctc 1920agttaattgc agcagcgaga aaccattgtc tttttcagct gtgtttagca catcaaaatc 1980agtttctaca ccacagtcaa caggttctgc tgctactatg acagcattgg cagcaacaaa 2040aacttctagt ttggctgatg attttggaga attcagcctt tttggggaat attctggtct 2100agcacctgtt ggggagcagg atgactttgc agattttatg gctttcagta atagctctat 2160ttcatctgag caaaagccgg atgacaaata tgatgccctt aaagaggaag ccagtcctgt 2220tcctctaacc agcaacgtgg gcagcacagt gaagggtgga caaaactcga ctgctgcgtc 2280taccaagtac gatgtcttca gacaactttc tctggaaggg tctggactag gtgttgaaga 2340cctgaaagat aacactcctt caggaaaaag tgatgatgat tttgctgact tccactccag 2400taaattttct tccataaact cggacaaatc cctgggagag aaagcagtgg ctttcagaca 2460caccaaagaa gactctgcat cagtgaagtc cttagatctc ccttccattg gtggcagcag 2520tgttggcaag gaggactctg aagatgcact ctctgttcag tttgacatga aattggctga 2580tgtgggagga gatcttaagc atgtcatgtc tgatagctct ttggatttac caacagttag 2640tggccagcat cctcctgctg cagcaggaag tggatccccc tcagccacct caattcttca 2700aaagaaagag acttcatttg gcagttctga aaacatcacc atgacatctc tctccaaagt 2760aacgaccttt gtaagtgaag atgctcttcc agagaccacc ttcccagctc ttgccagttt 2820taaagacacg attcctcaga ccagtgagca aaaggaatat gaaaacagag actataaaga 2880tttcacaaaa caggacctgc ctacggctga acggagccag gaggccacgt gtcccagccc 2940agcgtccagt ggtgcctctc aagaaacccc gaacgaatgt tcggatgact ttggagagtt 3000tcaaagtgaa aagcccaaaa tcagcaaatt tgacttctta gtagccactt cacaaagcaa 3060aatgaaatcc agtgaagaaa tgatcaaaag tgagctggca acctttgacc tttctgttca 3120aggatcacac aagaggagtt tgagccttgg tgataaagaa ataagccgtt cttctccttc 3180tccagctttg gagcagcctt tcagagaccg ttccaatact ctgaatgaga agcccgccct 3240gcccgtcatc cgagacaagt acaaagacct gacgggagag gtggaggaaa atgagagata 3300tgcatatgaa tggcagagat gcctggggag tgccctgaat gtcattaaga aggcaaatga 3360taccttaaat ggaatcagta gtagttctgt ttgcacagaa gtaattcagt cagctcaagg 3420catggaatat ttattaggtg ttgttgaagt gtacagggta accaagcgtg tggagctggg 3480gataaaagcc actgcagtgt gcagtgagaa actccagcag ttgctgaagg acatcgataa 3540agtgtggaat aacctaatcg gcttcatgtc actcgccaca ctcacaccag atgaaaactc 3600gctggatttt tcctcctgta tgttacggcc tgggattaaa aatgctcagg agcttgcctg 3660tggagtgtgc ctcttgaatg tggactcgag gagccggaaa gaagagaagc ctgcagaaga 3720acatcctaaa aaagcattca actcagaaac agacagtttc aagctggcct atggagggca 3780ccagtatcac gccagctgtg ccaacttctg gatcaactgt gtcgaaccaa agcctcctgg 3840cctcgtcctg cctgacctgc tctgaacaac tcctctgtga agcattgact tttttttttc 3900tgtgacaccc cacggggtga cagggaccaa taaatagaat gcgagcactg cacagttcgc 3960ttccctgaat cgatatgaag aacaccgcaa gggacggggc ccccgtcatc cccatggcca 4020gtctgcagga cttcaggtaa aattgtccca cccaaactgc acgtggcacc agaagcttgc 4080tcacttatct ctacttaaga ttttctgaaa tacggaccac ggctttcttg atctaaggaa 4140gaacttgctg ctgcagtatt gaaactgtga agaactgaca tttgaagaaa aatagattac 4200cgttgcggga ctagaatggg cgactgcttg gagccagtgc ttgtttttat ctaggacact 4260tactgtcctg tgaagtagaa tacatttatc tgcatttagt ttgttaatgt ctgaaatgaa 4320taaaaagagg aaattgcgat taaactgatg ttctgctttt tatggagaag attctgccca 4380tctcccctgg acagtagcag gcaggtgagg gcagatttta cccacttggt tgtcacaact 4440gaaccagttc tctactcctt cccttcactt ctgtccactg cactccagcc tgggcaacaa 4500gagcgaaact ctgtctcaaa aataaaaaat tccctttaac accttcaagg tcaaatgcct 4560gcctttgtga acagttaata aactttgaca ttttcagaca tttgccattc agaagggagc 4620attgtagcct gctgtagacc attccagcaa atgtcagaat gcagggcaag atgtgtgtcg 4680actatgtttt ttatgtttaa gttacttact tatttcttca ggtaagtgtg taccaaataa 4740caatactgaa aagccctccc cttgccaggc cgaggaaata aagcttaagt gaaacagctc 4800ttgggggaaa aatgccactt tacaaatact tttctaacaa atagcattat aatgaagttt 4860ttacttaatt ccattattta tatgttgacg ggaatgtaag tggttaaaaa gtattcatgt 4920gggacatctc attactttgt agctgtggct ttattaacca gtgaatgctg tggcccttag 4980cgaaatgcgt tgtcttctgc gtgatgtgga attagcgctg tattttaaaa gagggggg 5038<210> SEQ ID NO 37 <211> LENGTH: 2083 <212> TYPE: DNA <213> ORGANISM:Homo sapiens <220> FEATURE: <221> NAME/KEY: misc_feature <223> OTHERINFORMATION: Incyte ID No: 7481808CB1 <400> SEQUENCE: 37 aggggttgagcgggatgatc tggttcaatg tttcagagtg taaactggcc acccccacag 60 ggctccatcacaggaggccc cctcctgtgg ctcccctcct ctcctcccca gacctcccgt 120 cccctcccaccttcccatgc accccctccc ctcctcctat gcgctccctc cttcccacaa 180 accacttatcacctccacag ccctctgtca cctccggccc accagcctcc tcacctggga 240 gcagggccacatgatggtgg caaaaataac tccctttgac aaagtgtgaa gggggcagag 300 ggaggagggaagctgagccc cagcgctagg aaggagctct gagagggttc tgagctctgg 360 gtcaccctcactcactgggg acacagcagt cacgggctct gccctcatga gtgcgtaccc 420 actgccagcagcagcaactc acactgggtg aagtagctcc cagagcggta agggccggga 480 gctggactgactcccaacac acccagtccc ctccaaagcc tgccacaacc ctccaggctg 540 aggactcccccagcccctcc ctcaaccctg cgctctgtcc tcaggtccct gcatggtatc 600 agcgatgcttcttcacccca tttccgaggc cgggtgcgtt cccgccagcc ccagtcctca 660 ggcatttctctgagtctccg cccaccgccc cccgtctggg tccccatggc gggcactgcg 720 gcagcaggtgggcagcctcc ccgggttagc atgcaggagc acatggccat cgatgtgagc 780 ccgggccccatccggcccat ccgcctcatt tcccactact tcccgcactt ttaccctttt 840 gcggagcctgccctgcaccc tccgaacctg cgccccgcag cggcgtccgc cgtccgctct 900 gcaccccagctgcagcccga cccagagcca gaaggagact cagacgacag cactgccctg 960 ggcaccctggagttcacact tctttttgaa gcggacaaca gtgccctgca ttgcacggct 1020 catcgtgccaagggcctcaa gccattggcc tcaggctccg cggatgccta tgtcaaagcc 1080 aatctgctgccaggggccag caaggccagc cagcttcgga cacacaccgt tcggggcacg 1140 agggtacctgtctgggagga gacactcacc tatcacggct tcacccgcca ggatgctgag 1200 tgcaagacccttaggtctga cctgggcggc caccaggctg tgtgtgtgcg aggacccatg 1260 gtacagcgacagtggcaggc accttccctg ggggagctgc gggtgcccct gaggaagctg 1320 gtgccaaaccgagccaggag ctttgacatc tgtctggaga agcggaggct ggccaagagg 1380 cccaagagcctggacacagc ctgtggcatg tccctctatg aggaggaggt ggagacagag 1440 gtggcctgggaggaatgtgg gcacgtccta ctgtcactgt gctacagctc tcagcagggt 1500 ggcttgctggtaggtgtgct gcgctgcgcc cacctggccc ccatggatgc caatggttac 1560 tcggaccccttcgtgcgcct tttcctgcat ccaaatgcag ggaagaaatc taaattcaaa 1620 accagtgttcacaggaagac cctgaacccc gagttcaatg aggaattctt ttactcaggc 1680 ccacgggaggagctggccca gaagacgctg ctggtgtctg tgtgggacta tgacctaggc 1740 acggctgatgacttcattgg cggggtgcag ctgggcagcc atgccagtgg ggagcgcctg 1800 cggcactggcttgagtgcct gggccacagt gaccaccgcc tggagctgtg gcacccgctg 1860 gacagcaagcctgtccagct cagcgactag cccatgggcc ctgcctgccg cccctccact 1920 acagctgcctgaaacgtccc cacaaaaatg atggcggctg gggctgcctt accctcatgc 1980 ccagccccaagtcagagagg tgtttcctct ctccccgctt tcacattcac cccaccccaa 2040 atcatggagccgaaataaac atctccttca agccaggaaa aaa 2083 <210> SEQ ID NO 38 <211>LENGTH: 3615 <212> TYPE: DNA <213> ORGANISM: Homo sapiens <220> FEATURE:<221> NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte ID No:7488221CB1 <400> SEQUENCE: 38 agcggagctt ccagccaaaa tggcggagaacagcgagagt ctgggcaccg tccccgagca 60 cgagcggatc ttgcaggaga tcgagagcaccgacaccgcc tgtgtggggc ccaccctccg 120 gtctgtgtat gatgaccaac caaatgcgcacaagaagttt atggaaaagt tagatgcttg 180 tatccgtaat catgacaagg aaattgaaaagatgtgtaat tttcatcatc agggttttgt 240 agatgctatt acagaactcc ttaaagtaaggactgatgca gaaaaactga aggtgcaagt 300 tactgatacc aaccgaaggt ttcaagatgctggaaaagag gtgatagtcc acacagaaga 360 tatcattcga tgtagaattc agcagagaaatattacaact gtagtagaaa aattgcagtt 420 atgccttcct gtgctagaaa tgtacagtaagctgaaagaa cagatgagtg ccaaaaggta 480 ctattctgcc ctaaaaacta tggaacaattagagaatgtg tactttccct gggttagtca 540 ataccggttt tgtcagctca tgatagaaaatcttcccaaa ctccgtgagg atattaaaga 600 aatctccatg tctgatctca aagactttttggaaagtatt cgaaaacatt ctgacaaaat 660 aggtgaaaca gcaatgaaac aggcacagcatcagaaaacc ttcagtgttt ctctgcagaa 720 acaaaataaa atgaaatttg ggaaaaatatgtatataaat cgtgatagaa ttccagagga 780 aaggaatgaa actgtattga aacattcacttgaagaagag gatgagaatg aagaagagat 840 cttaactgtt caggatcttg ttgatttttcccctgtttat cgatgtttgc acatttattc 900 tgttttgggt gacgaggaaa catttgaaaactattatcga aaacaaagaa agaaacaagc 960 aagactggta ttgcaacccc agtcgaatatgcatgaaaca gttgatggct atagaagata 1020 tttcactcaa attgtagggt tctttgtggtagaagatcac attttacatg tgacccaagg 1080 attagtaacc agggcataca ctgatgaactttggaacatg gccctctcaa agataattgc 1140 tgtccttaga gctcattcat cctattgcactgatcctgat cttgttctgg agctgaagaa 1200 tcttattgta atatttgcag atactttacagggttatggt tttccagtga accgactttt 1260 tgacctttta tttgaaataa gagaccaatacaatgaaaca ctgcttaaga aatgggctgg 1320 agttttcagg gacatttttg aagaagataattacagcccc atccctgttg tcaatgaaga 1380 agaatataaa attgtcatca gcaaatttccctttcaagat ccagaccttg aaaagcagtc 1440 tttcccaaag aaattcccca tgtctcagtcagtgcctcat atttacattc aagttaaaga 1500 atttatttat gccagcctta aattttcagagtcactacac cggagctcaa cagaaataga 1560 cgatatgctt agaaaatcaa caaatctgctgctgaccaga actttgagta gctgtttact 1620 gaaccttatt agaaaacctc atataggtttgacagagctg gtacaaatca tcataaacac 1680 aacacacctg gagcaagctt gtaaatatcttgaggacttt ataactaaca ttacaaatat 1740 ttcccaagaa actgttcata ctacaagactttatggactt tctactttca aggatgctcg 1800 acatgcagca gaaggagaaa tatataccaaactgaatcaa aaaattgatg aatttgttca 1860 gcttgctgat tatgactgga caatgtctgagccagatgga agagctagtg gttatttaat 1920 ggaccttata aattttttga gaagcatctttcaagtgttt actcatttgc ctgggaaagt 1980 tgctcagaca gcttgcatgt cagcctgccagcatctgtca acatccttaa tgcagatgct 2040 actggacagt gagttaaaac aaataagcatgggagctgtt cagcagttta acttagatgt 2100 catacagtgt gaattgtttg ccagctctgagcctgtgcca ggattccagg gggataccct 2160 gcagctagca ttcattgacc tcagacaactccttgacctg tttatggttt gggattggtc 2220 tacttaccta gctgattatg ggcagccagcttctaagtac cttcgggtga atccaaacac 2280 agcccttact cttttggaga agatgaaggatactagcaaa aagaacaata tatttgctca 2340 gttcaggaag aatgatcgag acaaacagaagttgatagag acagtcgtga aacagctgag 2400 aagtttggtg aatggtatgt cccagcacatgtagacctca catggcttgc actcagtgac 2460 accaaatcca tgattcaatg ttgatcttgagcaagtattg gtcatgatac agtaatttgt 2520 ttacagaatc caaaaataca atagagaagatacatgaggg cttaaacaag aaatagtaat 2580 aaatatcatt tgtatggatt tttaaataatcgaatactat tttatatatg gaaaaaaatg 2640 accatttttt cacttttagg ggaaaatgcaaaagtgtaat acataaattg tcacaaatta 2700 tacctgaaat tgattacaaa tacatttgaaaaacatatgc ctctactcat aagtattttt 2760 ttctatttag acttgaatga taatctgttttttgatcagt atatggcttt ggaattcaat 2820 catgtctgat atggtagtat ttcactaccattttctgact tttagctttt attttcacct 2880 caatgtgatt taagcagacc aaaatttctaattctgctaa ttctgaaggg gaaatagaca 2940 aatcttaaaa gctgcctgaa atcaaacttgatttaactca gtaagaatgt gaattatttg 3000 ttctacttgg gtggtttaat ttaatcgttctgaatatgaa caaaaggttt tggattttct 3060 aaagatgcag tgttgtttct gttcatcagggttaatattt ctaactatat tgcttgtagg 3120 tgaccccatt ctggatttgt ttggtttggtttggttccag ttaaaagaga ggacaggaac 3180 taaatggggc taaccacttc aggtgcagcttgtgcgaggg tagatggttc ctgcacacag 3240 aagttaccac aggggtcagg ttactttcttcaaatagcag atttcagtac tttatcctca 3300 ttgtggaaac aagccaaacc aaatgaactctggaaaacct aaaacaaatg tacattttcc 3360 tttgtgtatg tttctgtggt ccaaatggcaatataaatcc agtctttatt ctccctttgt 3420 tgtatttatg ctgaatcttc cctttgccttttcaggattt aggcctgtaa gaaactatgc 3480 ctgattctgt aaaataagtg taaagaattatatgtacatc tctggatttt gtgatgaaat 3540 attaaaaata ttgagcaagt tgttgaaaaaaaaaaaaaaa aaaaaaaaaa aattctgcgg 3600 cgcaagaatt cagtg 3615 <210> SEQ IDNO 39 <211> LENGTH: 1194 <212> TYPE: DNA <213> ORGANISM: Homo sapiens<220> FEATURE: <221> NAME/KEY: misc_feature <223> OTHER INFORMATION:Incyte ID No: 7505894CB1 <400> SEQUENCE: 39 ctgctggttt cattcgaggtttcgggccga ggatgccagc ccccatcaga ttgcgggagc 60 tgatccggac catccggacagcccgaaccc aagctgaaga acgagaaatg atccagaaag 120 aatgtgctgc aatccggtcatcttttagag aagaagacaa tacataccga tgtcggaatg 180 tggcaaaatt actgtatatgcacatgctgg gctaccctgc tcactttgga cagttggagt 240 gcctcaagct tattgcctctcaaaaattta cagacaaacg cattgtccca gcatttaaca 300 cggggaccat cacacaagtcattaaagttc tgaaccctca gaagcaacag ctgcgaatgc 360 ggatcaagct tacatataatcacaagggct cagcaatgca agatctagca gaggtgaaca 420 actttccccc tcagtcctggcaatgagggt ttggcaccat tctcattctt tatcccactc 480 aatcaaagga actctgggaaggaggttgtg attgctggca agtccccccc aactgtacca 540 cgggcatgag gagctgaagagaactgctga ggaggatttt cctaaagtta ctgctgacct 600 tgaagcattg ttaaagactaatgtcctctc ctccactgtt gaggctggct gcttctggag 660 gctactttgc actcttcctcttctcctttt tccgcacttc tccacccctc ccacatttac 720 agccagaatc aacattccctgggcccctga ggaaataagc agctggtctg gaggagagga 780 ctgcaatcca tggcgaaaaaacactcactt tgtctctgca gcaaagagtt gccccttctt 840 tctactgttg tttctctgtggactgggcaa ggtggggtat ttattcctca ctagctgggt 900 taccatcttc aggcacttttaacatctggc attcggaatg gaaatgtaat aatggacatt 960 aggggagccc tgccctttttctactggttc ccccaatgtt tgaaagaggc attaggctcc 1020 tggtagccct tttctgtgcattgctgttta cacccagaca cacacatggt atgtttgtta 1080 ccaagaactg gtcaaaaccttgcggagttt attttgtaaa cacctgggac aaatgggagg 1140 ttaaaaggaa gcttttggtcgagaattttg gcatgaaagg gatatggtgg ctcc 1194 <210> SEQ ID NO 40 <211>LENGTH: 1306 <212> TYPE: DNA <213> ORGANISM: Homo sapiens <220> FEATURE:<221> NAME/KEY: misc_feature <223> OTHER INFORMATION: Incyte ID No:7505901CB1 <400> SEQUENCE: 40 gccccgaatt tatcacggag gggcggggctgaggctgcgg gagctggagc ggggaagaaa 60 agggaattcc aacctgtgga accttggggggtccccgggg tcggcgcctt cccattgact 120 gtgggcggtg caagggacgg agcctctggcggctcgtggg ggtgttgggg tccgcagggg 180 gagggagggg agtgtcagag tgtgagcggggtacgggaat tccaaatttg agggcctccc 240 ggctctggcg ccggggaggg agagctcaggccgccatgcg ggacaggacc cacgagctga 300 gacaggggga tgacagctcg gacgaagaggacaaggagcg ggtcgcgctg gtggtgcacc 360 cgggcacggc acggctgggg agcccggacgaggagttctt ccacaaggtc cggacaattc 420 ggcagactat tgtcaaactg gggaataaagtccaggagtt ggagaaacag ctgaaggcca 480 tagagcccca gaaggaggaa gctgatgagaactataactc cgtcaacaca agaatgagaa 540 aaacccagca tggggtcctg tcccagcaattcgtggagct catcaacaag tgcaattcaa 600 tgcagtccga ataccgggag aagaacgtggagcggattcg gaggcagctg aagatcacca 660 atgctgggat ggtgtctgat gaggagttggagcagatgct ggacagtggg caaagcgagg 720 tgtttgtgtc caatatcctg aaggacacgcaggtgactcg acaggcctta aatgagatct 780 cggcccggca cagtgagatc cagcagcttgaacgcagtat tcgtgagctg cacgacatat 840 tcacttttct ggctaccgaa gtggagatgcagggggagat gatcaatcgg attgagaaga 900 acatcctgag ctcagcggac tacgtggaacgtgggcagga gcacgtcaag acggccctgg 960 agaaccagaa gaaggcgagg aagaagaaagtcttgattgc catctgtgtg tccatcaccg 1020 tcgtcctcct agcagtcatc attggcgtcacagtggttgg ataatgtcgc acattgttgg 1080 cactaggagc accaggaacc cagggcctggccttctctcc cagcagcctg gggggcaggg 1140 cagagcctcc agtcggaccc cttcctcacactggccccta tgcagaaggg cagacagttc 1200 ttctggggtt ggcagctgct cattcatgatggcctcctcc ttcaggcctc aatgcctggg 1260 ggaggcctgc actgtcctga ttggccgggacacacggttt tgtaaa 1306

1. An isolated polypeptide selected from the group consisting of: a) apolypeptide comprising an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20, b) a polypeptide comprising a naturallyoccurring amino acid sequence at least 90% identical to an amino acidsequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2,SEQ ID NO:7-9, SEQ ID NO:14, and SEQ ED NO: 17, c) a polypeptidecomprising a naturally occurring amino acid sequence at least 92%identical to the amino acid sequence of SEQ ID NO:6, d) a polypeptidecomprising a naturally occurring amino acid sequence at least 94%identical to the amino acid sequence of SEQ ID NO:18, e) a polypeptidecomprising a naturally occurring amino acid sequence at least 95%identical to the amino acid sequence of SEQ ID NO:5, f) a polypeptidecomprising a naturally occurring amino acid sequence at least 96%identical to the amino acid sequence of SEQ ID NO:10, g) a polypeptidecomprising a naturally occurring amino acid sequence at least 98%identical to the amino acid sequence of SEQ ID NO:4, h) a polypeptideconsisting essentially of a naturally occurring amino acid sequence atleast 90% identical to an amino acid sequence selected from the groupconsisting of SEQ ID NO:11-13, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:19,and SEQ ID NO:20, i) a biologically active fragment of a polypeptidehaving an amino acid sequence selected from the group consisting of SEQID NO:1-20, and j) an immunogenic fragment of a polypeptide having anamino acid sequence selected from the group consisting of SEQ IDNO:1-20.
 2. An isolated polypeptide of claim 1 comprising an amino acidsequence selected from the group consisting of SEQ ID NO:1-20.
 3. Anisolated polynucleotide encoding a polypeptide of claim
 1. 4. Anisolated polynucleotide encoding a polypeptide of claim
 2. 5. Anisolated polynucleotide of claim 4 comprising a polynucleotide sequenceselected from the group consisting of SEQ ID NO:21-40.
 6. A recombinantpolynucleotide comprising a promoter sequence operably linked to apolynucleotide of claim
 3. 7. A cell transformed with a recombinantpolynucleotide of claim
 6. 8. (CANCELLED)
 9. A method of producing apolypeptide of claim 1, the method comprising: a) culturing a cell underconditions suitable for expression of the polypeptide, wherein said cellis transformed with a recombinant polynucleotide, and said recombinantpolynucleotide comprises a promoter sequence operably linked to apolynucleotide encoding the polypeptide of claim 1, and b) recoveringthe polypeptide so expressed.
 10. A method of claim 9, wherein thepolypeptide comprises an amino acid sequence selected from the groupconsisting of SEQ ID NO:1-20.
 11. An isolated antibody whichspecifically binds to a polypeptide of claim
 1. 12. An isolatedpolynucleotide selected from the group consisting of: a) apolynucleotide comprising a polynucleotide sequence selected from thegroup consisting of SEQ ID NO:21-40, b) a polynucleotide comprising anaturally occurring polynucleotide sequence at least 90% identical to apolynucleotide sequence selected from the group consisting of SEQ IDNO:21, SEQ ID NO:22, and SEQ ID NO:25-39, c) a polynucleotide comprisinga naturally occurring polynucleotide sequence at least 97% identical tothe polynucleotide sequence of SEQ ID NO:24, d) a polynucleotidecomprising a naturally occurring polynucleotide sequence at least 98%identical to the polynucleotide sequence of SEQ ID NO:40, e) apolynucleotide complementary to a polynucleotide of a), f) apolynucleotide complementary to a polynucleotide of b), g) apolynucleotide complementary to a polynucleotide of c), h) apolynucleotide complementary to a polynucleotide of d), and i) an RNAequivalent of a)-h).
 13. (CANCELLED)
 14. A method of detecting a targetpolynucleotide in a sample, said target polynucleotide having a sequenceof a polynucleotide of claim 12, the method comprising: a) hybridizingthe sample with a probe comprising at least 20 contiguous nucleotidescomprising a sequence complementary to said target polynucleotide in thesample, and which probe specifically hybridizes to said targetpolynucleotide, under conditions whereby a hybridization complex isformed between said probe and said target polynucleotide or fragmentsthereof, and b) detecting the presence or absence of said hybridizationcomplex, and, optionally, if present, the amount thereof. 15.(CANCELLED)
 16. A method of detecting a target polynucleotide in asample, said target polynucleotide having a sequence of a polynucleotideof claim 12, the method comprising: a) amplifying said targetpolynucleotide or fragment thereof using polymerase chain reactionamplification, and b) detecting the presence or absence of saidamplified target polynucleotide or fragment thereof, and, optionally, ifpresent, the amount thereof.
 17. A composition comprising a polypeptideof claim 1 and a pharmaceutically acceptable excipient.
 18. Acomposition of claim 17, wherein the polypeptide comprises an amino acidsequence selected from the group consisting of SEQ ID NO:1-20. 19.(CANCELLED)
 20. A method of screening a compound for effectiveness as anagonist of a polypeptide of claim 1, the method comprising: a) exposinga sample comprising a polypeptide of claim 1 to a compound, and b)detecting agonist activity in the sample. 21-22. (CANCELLED)
 23. Amethod of screening a compound for effectiveness as an antagonist of apolypeptide of claim 1, the method comprising: a) exposing a samplecomprising a polypeptide of claim 1 to a compound, and b) detectingantagonist activity in the sample. 24-25. (CANCELLED)
 26. A method ofscreening for a compound that specifically binds to the polypeptide ofclaim 1, the method comprising: a) combining the polypeptide of claim 1with at least one test compound under suitable conditions, and b)detecting binding of the polypeptide of claim 1 to the test compound,thereby identifying a compound that specifically binds to thepolypeptide of claim
 1. 27. (CANCELLED)
 28. A method of screening acompound for effectiveness in altering expression of a targetpolynucleotide, wherein said target polynucleotide comprises a sequenceof claim 5, the method comprising: a) exposing a sample comprising thetarget polynucleotide to a compound, under conditions suitable for theexpression of the target polynucleotide, b) detecting altered expressionof the target polynucleotide, and c) comparing the expression of thetarget polynucleotide in the presence of varying amounts of the compoundand in the absence of the compound.
 29. A method of assessing toxicityof a test compound, the method comprising: a) treating a biologicalsample containing nucleic acids with the test compound, b) hybridizingthe nucleic acids of the treated biological sample with a probecomprising at least 20 contiguous nucleotides of a polynucleotide ofclaim 12 under conditions whereby a specific hybridization complex isformed between said probe and a target polynucleotide in the biologicalsample, said target polynucleotide comprising a polynucleotide sequenceof a polynucleotide of claim 12 or fragment thereof, c) quantifying theamount of hybridization complex, and d) comparing the amount ofhybridization complex in the treated biological sample with the amountof hybridization complex in an untreated biological sample, wherein adifference in the amount of hybridization complex in the treatedbiological sample is indicative of toxicity of the test compound.30.-95. (CANCELLED)